https://noisebridge.net/api.php?action=feedcontributions&user=Turbclnt&feedformat=atomNoisebridge - User contributions [en]2016-12-09T17:22:35ZUser contributionsMediaWiki 1.19.1https://noisebridge.net/wiki/Category:EventsCategory:Events2011-05-24T00:57:48Z<p>Turbclnt: /* Upcoming Events edit */</p>
<hr />
<div>&lt;!-- Note that this page uses transclusion. Content between the &quot;onlyinclude&quot; tags below will be pushed to the main page --&gt;<br />
Official, Semi-Official, one-off and other events at the Noisebridge space.<br />
<br />
=Event Calendar=<br />
Not all events make it onto this calendar. Many events only make it to the Discussion or Announcements [[Mailinglist | mailing lists]], [[IRC]] or in person at [[:Category:Meeting_Notes | Tuesday meetings]]. Best of all, Noisebridge is about people getting together at the space in San Francisco to do stuff... like in person. Some events just happen. Pay attention!<br />
<br />
If you'd like to host an event yourself, we have advice on [[Hosting_an_Event | hosting an event]] at Noisebridge.<br />
<br />
Event posters are encouraged to crosspost to the Google Calendar. View the [http://www.google.com/calendar/embed?src=vo3i3c0qtjnkjr2ojasd0ftt8s%40group.calendar.google.com&amp;ctz=America/Los_Angeles Google Calendar], view the [http://www.google.com/calendar/feeds/vo3i3c0qtjnkjr2ojasd0ftt8s%40group.calendar.google.com/public/basic Google Calendar in XML], or the [http://www.google.com/calendar/ical/vo3i3c0qtjnkjr2ojasd0ftt8s%40group.calendar.google.com/public/basic.ics Google Calendar in ical] format.<br />
<br />
To post Google Calendar entries for your event, contact a Noisebridge member for access.<br />
<br />
(Wouldn't it be great if there were a gCal mediawiki plugin so crossposting wasn't needed? Do you know of a good one? Help us!) &lt;- working on this, need to upgrade Mediawiki in order to use some plugins.<br />
&lt;!-- Items inside this &quot;onlyinclude&quot; tag will be pushed to the main page --&gt;&lt;onlyinclude&gt;<br />
=== Upcoming Events &lt;small&gt;[https://www.noisebridge.net/index.php?title=Category:Events&amp;action=edit&amp;section=2 edit]&lt;/small&gt; ===<br />
<br />
*'''May 18th, 6:30-9pm, Wednesday''' - Gephi Workshop in the main area. Gephi is an open-source software for network visualization and analysis. It helps data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. Bring your own laptop. More info: http://www.meetup.com/VisualizeMyData/events/17216797/<br />
<br />
*'''May 19th, 8-9:30pm, Thursday''' - [https://www.noisebridge.net/wiki/Five_Minutes_of_Fame Five Minutes of Fame!] Noisebridge's monthly series of lightning talks focused on hacking, making, and other things that waste finite quantities of entropy!<br />
<br />
*'''May 21-22, 10am-6pm (approx), Saturday &amp; Sunday''' - Maker Faire! While not held at Noisebridge, many of our members will be there. Noisebridge will have a booth in the Hackerspace area. More info: http://makerfaire.com/bayarea/2011/. [[User:maltman23|Mitch]], with the help of 35 volunteers, will be teaching 3,000 people to solder at the Hardware Hacking Area (look for the tent in back of the Maker Shed at the Faire).<br />
<br />
*'''May 28, 1pm-4pm, Saturday''' - As part of [http://whatwillyoulearn.com/catalog Workshop Weekend], [[User:maltman23|Mitch]] will be giving a workshop to teach people how to solder using his Trippy RGB Waves kit (make waves of colors by waving your hand!), designed for people who've never made anything with electronics. More info: http://whatwillyoulearn.com/catalog<br />
<br />
*'''May 28, 4pm-5:30pm, Saturday''' - As part of [http://whatwillyoulearn.com/catalog Workshop Weekend], [[User:turbclnt|Sean]] will be giving a workshop to teach people how to distill using the Noisebridge 25L distillation setup! Aimed at complete beginners. More info: http://whatwillyoulearn.com/catalog<br />
<br />
*'''May 29, 1pm-4pm, Sunday''' - As part of [http://whatwillyoulearn.com/catalog Workshop Weekend], [[User:maltman23|Mitch]] will be giving a workshop to teach people how to solder using his TV-B-Gone kit (turn off TVs in public places up to 50 yards away!), designed for people who've never made anything with electronics. More info: http://whatwillyoulearn.com/catalog<br />
<br />
*'''May 31st, 7pm , Tuesday''' - Vegan Hacker. This month's hack: Corn Dogs! More info: http://www.veganhackerSF.com<br />
<br />
*'''UPDATE: June 5 or 6, 2:00pm - 5:00pm''' - The San Francisco Chapter of [http://toool.us The Open Organisation Of Lockpickers] invite you to join us to learn about the history, styles, features, and techniques for using Bogota wave rakes. This meeting focuses on the unique characteristics and effectiveness of Bogota tools. Christina Palmer will demonstrate both picking and how to make your own set of Bogota rakes from stainless steel windshield wiper blade inserts. Afterward, she'll entertain Bogota-related Q&amp;A and, for those new to lockpicking, questions about basic tools and techniques. Final date available shortly.<br />
<br />
=== Recurring Events &lt;small&gt;[https://www.noisebridge.net/index.php?title=Category:Events&amp;action=edit&amp;section=3 edit]&lt;/small&gt; ===<br />
&lt;!-- Large turnout events should be written in '''bold'''. --&gt;<br />
* '''Monday'''<br />
** [[House_Keeping#Trash_and_Recycling|Trash Night]] - Take out the trash and compost for Tuesday morning!<br />
** 18:00 [[iPhone OS developer weekly meetup]] - UPDATE!!! moved to Sandbox suites pending bedbug issue. We make teh applukashuns, joyn us 2 make dem 2! [http://meetup.com/iphonedevsf meetup page]<br />
** 18:30 [[PyClass]] - Learn how to program using the Python programming language.<br />
** '''19:00 [[Circuit Hacking Mondays]]''' - Learn to solder! Mitch will bring kits to make cool, hackable things that you can bring home after you make them. Bring your own projects to hack! There's now an Audio Hacking Adjunct group that meets along with the Circuit Hackers. <br />
* '''Tuesday'''<br />
** 12:30 [[Django Study Group]] - install and use the Django Python-based web framework, Turing classroom <br />
** 15:00 [[Linux System Administration Study Group]] wiki page - Study Linux admining in the Turing classroom.<br />
** 18:00 [[Tastebridge]] Last Tuesday of every month: Vegan Hacker: Vegan Cooking Class. More info http://www.veganhackerSF.com. <br />
** 18:00 Introduction to C Programming, Turing Classroom <br />
** 19:00 [[german_corner|German Corner]] Learn and practice speaking German.<br />
** 19:00 [[ruby_class|Ruby Class]] 7pm-9pm<br />
&lt;!--On haitus? Pls update ** 19:00 [[Origami|Learn You A Origami!]] - Learn how make folded-paper models. Beginners welcome!--&gt;<br />
&lt;!-- On hiatus as of 3/29/2011 ** 19:30 [[Probability]] study group --&gt;<br />
&lt;!-- On hiatus -- pls update 3/29/11 ** 19.30 [[Show and Tell]] -- Show your latest and greatest projects and hacks (working or in-progress), just before the weekly meeting. We meet in the Electronics Lab/Main Space. --&gt;<br />
** '''20:00 [[#Meetings|Noisebridge Weekly Meeting]]''' - Introducing new people and events to the space, general discussion, and decision making.<br />
* '''Wednesday''' <br />
** 17:00 Introduction to C Programming, Turing classroom (review of last Tuesday, preview of next Tuesday) <br />
** 18:00 [[LinuxDiscussion|Linux Discussion]] - Linux meetup in the Turing classroom.<br />
&lt;!--Weekly? Pls update ** 17:00 [[BarCamp Staff Meeting]] - Meeting for BarCamp Staff to discuss plans for San Francisco BarCamp.--&gt;<br />
** 18:00 [[BioBridge]] Practical microbiology - we culture microbes for baking, brewing, fermentation and other yummy purposes. Come play and learn!<br />
** 19:00 [[SCoW]] - Sewing, Crafting, Or Whatever! Come make cool stuff with geeks.<br />
** 19:30 [[Machine Learning]] - Teach computers to learn stuff using artificial intelligence and other techniques.<br />
** 20:00 [[BACE Timebank]] (1st Wednesdays) - Help organize community mutual aid by trading in equal time credits. For more info email mira (at) sfbace.org or to join go to [http://timebank.sfbace.org timebank.sfbace.org].<br />
* '''Thursday'''<br />
** [[House_Keeping#Trash_and_Recycling|Trash Night]] - Take out the trash for Friday morning!<br />
** 19:00 [[Noisedroid/Nights]] - An Android-Themed Co-working Night.<br />
** '''20:00 [[Five_Minutes_of_Fame | Five Minutes of Fame]]''' (3rd Thursdays)<br />
** '''20:00 [[In-Depth]]''' (1st Thursdays)<br />
* '''Friday''' <br />
** 12:30 [[Django Study Group]] - install and use the Django Python-based web framework, Turing classroom <br />
** 15:00 [[Linux System Administration Study Group]] wiki page - Study Linux admining in the Turing classroom.<br />
* '''Saturday'''<br />
&lt;!-- hiatus? plz update ** 16:00 [[Pwn Your Own]] - Pwn Your Own is your chance to learn about every day security threats to every day internet activities. Designed for hackers at all levels, (1st Saturday). --&gt;<br />
** 12:00-18:00 - Noisebridge Hackathon! Second Saturday Hackathon is a casual monthly event dedicated to building community and working on the space or relevant projects. This is a great time to get feedback or help on any projects you have been considering that center around the space, culture, and infrastructure of Noisebridge. You can also help with existing projects and find out ways to get involved. (2nd Saturday)<br />
* '''Sunday'''<br />
** 14:00 [[Schemers]] - Explore the scheme programming language &amp; fundamental CS concepts using the classic [http://mitpress.mit.edu/sicp/ SICP].<br />
** 14:00 [http://baha.bitrot.info/ Bay Area Hacker's Association - security meeting] (2nd Sundays)<br />
** 15:00 [[Go]] - Playing of the Go boardgame. On nice days we often take the boards to Dolores Park and play there.<br />
** 15:00 [[Locks!]] - Lock sport, sundays when there is demand. ( See [[locks!]] for more information. )<br />
&lt;!--Happening? pls update ** 17:00 [[Rsync Users Group]] - A twelve step program for those who have poor *nix habits.--&gt;<br />
** 18:00 [[Spacebridge]] - Noisebridge's space program<br />
** 19:00 [[Hack Politics]] -- 1st and 3rd Sundays of the month. Hack the political systems.<br />
&lt;/onlyinclude&gt;<br />
<br />
=== Proposed Future Events and Classes ===<br />
<br />
:'''(TBD)''': [[Probability]] - Weekly probability study group based on [http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-041-probabilistic-systems-analysis-and-applied-probability-spring-2006/related-resources/ Fundamentals of Applied Probability Theory] by Al Drake<br />
:'''(TBD)''': [[German]] - Learn German, all levels. 7pm beginners, 8pm advanced. RSVP 24 hours in advance for the benefit of the instructor. Events ran May-November 2009 on Mondays. Currently on hiatus. Get on the mailing list.<br />
:'''(TBD)''': [[Mandarin Corner|Mandarin]] - Learn or practice Mandarin, all levels. Also currently on hiatus. Get on the mailing list.<br />
:'''(TBD)''': [[Movie Night!]] - [[User:ThOMG|Thom]] wants to build community through nerdy sci-fi! (+Bill+Ted+Excellence++)<br />
:'''(TBD)''': [[Introduction to the AVR Microcontroller]] - [[User:Mightyohm|Jeff]] and [[User:Maltman23|Mitch]] are planning an introductory class for people wanting to make cool projects with AVRs.<br />
:'''(TBD)''': [[Basic Chemistry Lab Techniques]]<br />
:'''(TBD)''': [[Cuddle Puddle for the Economy]] - Stress-hacking with informal massage exchange.<br />
:'''(TBD)''': [[Milk and Cookies]] - Come read your favorite selections out loud. With Milk and Cookies (and yeah, probably beer too).<br />
:'''(TBD)''': [[Processing Workshop 2]] - [[User:Scmurray|Scott]] is interested in teaching this, and is busy thinking about what, where, when, why, and how.<br />
:'''(TBD)''': [[Hack your Hardware]] -- We call BS on &quot;no user-serviceable parts inside&quot;<br />
:'''(TBD)''': [[Homebrew Instruction Class]] - The Wort (pt 1/3)<br />
:'''(TBD)''': [[Trip to Shooting Range]] - Field trip to a shooting range, to shoot guns. Express interest at [[Trip to Shooting Range]]<br />
:'''(TBD)''': [[Surface Mount Soldering Workshop]] - Learn how to solder cicuits with small surface mount parts. [[User:maltman23|Mitch Altman]] and Martin Bogomolni and others will show their tricks. [[User:maltman23|Mitch]] will bring hackable kits that uses surface mounts for you to solder.<br />
:'''(TBD)''' - [[Locksport and Lockpicking]]<br />
:'''(TBD)''' - [[Version control tutorial]]<br />
:'''(TBD)''' - [[Foreign language learning for rocket scientists]] - I'm near-native (fool people when I try) in (French and) Japanese, and a pro trans/terpreter and will share my shortcuts (skill-order, vocab, speed/articulation, translation≅grammar). No expertise on tonal languages yet... so if you know how to remember tones or how tone-sandhi interacts with speed and/or how nuances of speaker attitude are expressed in them (what we do with rythm/inflection/sentence-intonation and stress in Eng., and with particles and ??? in e.g. Cantonese) please chime in or call me (415-608-0564) so I can convey your wisdom. [also looking for a from-scratch Arabic partner]<br />
:'''(TBD)''': [[Getting started with Arduino]]<br />
:'''(TBD)''': [[Distributed Databases]]<br />
:'''(TBD)''': [[Scrum Club]] - I though I'd test the waters and see if anyone was interested in a noisebridge scrum club details are here http://scrumclub.org/scrum-clubs/ if inturested hit me up twitter: @theabcasian, facebook: http://www.facebook.com/theabcasian<br />
:'''(TBD)''': [[CNC Mill Workshop]] - Who wants to make stuff on the [[MaxNCMill]]?<br />
:'''(TBD)''': [[Math &amp; Science Help]] - If you would like some math, science or engineering help, I'm down to lend a hand.<br />
:'''(TBD)''': [[Cyborg Group|Cyborg Group / Sensebridge]] - Work on projects like artificial senses. Someone needs to lead this!<br />
:'''(TBD)''': [[OpenEEG]] - Brain tech. Has historically met on Sundays, at the behest of interested parties.<br />
:'''(TBD)''': [[Programming_for_Poets | Programming for Poets]] - Gentle intro to programming using Processing<br />
<br />
= Past Events =<br />
===2011===<br />
* '''April 13th, 19:00''' - Kombucha fermentation class with [[BioBridge]] <br />
*'''April 7th, 20:00''' - [[In-Depth|Noisebridge: In-Depth]] Our monthly lecture and round table. This month's speaker will be Aragorn! his lecture will be &quot;Anarchism &amp; technology: An unbridgeable chasm&quot;<br />
*'''April 4th, 20:00''' - Camp KDE Party. Come and meet part of the KDE North America community and get a quick overview of this year's [http://camp.kde.org/ Camp KDE] conference. There will be beer. <br />
*'''April 3rd, 16:00''' - NoiseCaching: Meet-up to build some geocaches, and talk about making geocoins. Then we'll head out to find some local caches and place caches we made. [http://www.geocaching.com More info about Geocaching here]<br />
* '''March 20th, 19:00''' [[Hack Politics]] meetup -- the first meetup to figure out how we in the hacker community can effectively mobilize and create meaningful change in these interesting times<br />
* '''March 12th, 12:00-18:00 - Noisebridge Hackathon!''' Second Saturday Hackathon is a casual monthly event dedicated to working on the space or relevant projects and building community. This is a great time to get feedback or help on any projects you have been considering that center around the space, culture, and infrastructure of Noisebridge. You can also help with existing projects and find out ways to get involved.<br />
* '''March 10, Thursday, 19:00 - Group Grammar Clinic''' - Church Classroom - Donations gladly accepted - A clinic for grammar and writing evaluation. Please bring your web/social or technical writing for us to evaluate. Bring your laptop as well. Collaboration groupware possibly provided. (Please suggest groupware software to use if you wish). Constructive feedback from other group members is encouraged so that this clinic is a group process. - Facilitator: [[User:Owen|Owen]] (opietro@yahoo.com)<br />
* '''March 9th, 20:00''' - Ferment and filter a mash! [[fermentation logs]]<br />
<br />
===2010===<br />
* '''Sunday, August 22, 19:00 CLUB-MATE DROPOFF AND TASTING PARTY''' Nick Farr will be in town to drop off Club-Mate ordered by San Franciscans!<br />
* '''June 5th, 12:00-19:00 - [[NoiseBridgeRehab]]''' - Help make the space more usable and accessible! Noisebridge needs your help!<br />
* '''June 5th, 16:00-20:00 - [[Science For Juggalos]]''' - Science Fair in front of the Warfield Theater teaching magnetism to Juggalos<br />
* '''June 6th, 15:00 - [[AVC Meetup]]''' - Entrepreneurial bonding &amp; matchmaking<br />
* '''June 9th, 21:00 - Your liver supports Noisebridge''' - Come to Elixir @ 16th &amp; Guerrero anytime after 21:00 and drink, drink, drink! 50% of tips go to Noisebridge<br />
* '''February 27th, 20:00 - [[Hacker EPROM]]''' - Noisebridge's first prom! Nice tie and a (robot) date required. We will have a DJ and punch.<br />
* '''February 24th, 19:00, Wednesday - Joris Peels, of [http://www.shapeways.com Shapeways]''', and expert on 3D printing, will give a [[ShaperwaysPresentation | talk and demonstration]] at Noisebridge!.<br />
* '''February 23rd, 18:00 - Cleaning day''' - Come and help clean Noisebridge, because everyone loves a clean hack space.<br />
* '''February 12th, 21:00 - visit from Steve Jackson'''. Game designer [http://en.wikipedia.org/wiki/Steve_Jackson_%28US_game_designer%29 Steve Jackson], founder of Steve Jackson Games, will visit Noisebridge.<br />
* '''January 27th, 18:00-20:00 - [[beatrixjar event|Circuit Bending Workshop]]''' - [http://www.beatrixjar.com/ Beatrix*JAR] (contact [[User:Gpvillamil|Gian Pablo]] for more info)<br />
* '''January 27th, 20:00-22:00 - [[beatrixjar event|Circuit Bending Performance]]''' - [http://www.beatrixjar.com/ Beatrix*JAR] - &quot;Celebrate a night of new sound that will change your idea of music forever!&quot;<br />
* '''January 25th, 19:30 - [[Bag Porn]]''' - What's in your bag?<br />
* '''January 20th, 19:00-21:00 - [http://groups.google.com/group/bacat/about Bay Categories &amp; Types]''' - Categories, monoids, monads, functors and more! Held in the Alonzo Church classroom.<br />
* '''January 20th, 19:00 - [[User Experience Book Club SF]]''' - Our book this month is &quot;A Theory of Fun for Game Design&quot; by Raph Koster - http://is.gd/6sEqw (meets in Turing)<br />
* '''January 21st, 20:00 - [[Five Minutes of Fame]]''' - Monthly set of lightning talks on diverse topics<br />
* '''January 22nd, 17:00 - [[CleaningParty| Cleaning Party]]''' - Come help clean up Noisebridge! Awsum fun!<br />
* ...January 14th,16th, and 17th 1:00- ??? Build Out day for kitchen/bathroom/laundry bring yourself and a good attitude, learn a few things as well<br />
* '''January 15th, 18:00 - [[CNC_Mill_Workshop]]''' - Learn to use the CNC mill for 2D engraving and circuit board routing<br />
* Thursdays 17:00 [[ASL Group|American Sign Language]] - Learn how to talk without using your voice (or just come chat in ASL). &lt;small&gt;[http://whenisgood.net/noisebridge/asl/generic click to reschedule]&lt;/small&gt;<br />
<br />
===2009===<br />
* '''November 18th, 19:30''' - [[Dorkbot_2009_11_18|Dorkbot]]<br />
* '''November 19th, 18:00''' - [[Mesh meetup]]<br />
* '''November 19th, 20:00''' - [[Five Minutes of Fame]]<br />
* '''November 20th, 18:00''' - Loud Objects [http://www.flickr.com/photos/createdigitalmedia/3428249036/ Noise Toy workshop].<br />
* '''November 20th, 20:00''' - Performance by [http://www.loudobjects.com/ Loud Objects], (featuring Tristan Perich and Lesley Flanigan) and [http://www.myspace.com/jibkidder Jib Kidder].<br />
:'''2009-11-05''' - [http://www.server-sky.com/ Server Sky presentation: Internet and Computation in Orbit] by Keith Lofstrom<br />
:'''2009-11-05''' - [[Mesh meetup]]<br />
:'''2009-11-02''' - [[French]] book club meeting to discuss [http://www.amazon.com/exec/obidos/tg/detail/-/2842612892/ref=ord_cart_shr?_encoding=UTF8&amp;m=ATVPDKIKX0DER&amp;v=glance Une Si Longue Lettre]<br />
: ''' October 1st, 18:00''' - [[Wireless_Mesh_Network_Meetup | Mesh wireless meetup]]<br />
: ''' October 1st, 19:00''' - [http://groups.google.com/group/bacat Bay Area Categories and Types]<br />
: '''2009-10-03''' [[Year 1 Open Hacker House]]<br />
:'''Friday''': [[CrazyCryptoNight]] - Discussion of cryptography for beginners through experts. 6-???<br />
:'''Sunday''' : [[OpenEEG | OpenEEG Hacking]] Sundays, at 3-5pm.<br />
:'''Tuesday''': [[Haskell/Haschool]] - Learn Haskell with Jason Dusek. 6PM - 7:30PM, from May until we're all experts.<br />
:'''Wednesday''': [[Adobe_Lightroom|Adobe Lightroom]] - Become a more organized photographer. Weekly class (mostly held off site).<br />
:'''Thursday''': [[Professional VFX Compositing With Adobe After Effects]] - Taught by [[User:SFSlim|Aaron Muszalski]]. 7:30PM - 10PM, most Thursdays in May &amp; June &amp; ? (click through dammit)<br />
:'''2009-09-17''': [[Five Minutes of Fame]] 3D Edition<br />
:'''2009-09-17''': [[Wireless Mesh Network Meetup | Mesh wireless meetup]]<br />
:'''2009-08-20''': [[Five Minutes of Fame]] One Dee Edition<br />
:'''2009-07-16''': [[Five Minutes of Fame]] Zero Dee<br />
:'''2009-07-02 - 2009-07-05''': [http://toorcamp.org Toorcamp]<br />
:'''2009-07-01''': Noisedroid meeting to discuss location logging on Android platform (and other stuff too, I'm sure)<br />
:'''2009-06-30''': [[Powerbocking Class|Powerbocking class]]<br />
:'''2009-06-30''': &quot;Suing Telemarketers for Fun and Profit&quot; (Toorcamp talk preview)<br />
:'''2009-06-28''': &quot;Meditation for Hackers&quot; (Toorcamp workshop preview)<br />
:'''2009-06-18''': [[Five Minutes of Fame]]<br />
:'''2009-06-15''': [[Eagle Workshop]] Session two of the Eagle CAD workshop.<br />
:'''2009-06-13''': [[RoboGames 2009]] Noisebridge had a booth staffed by vounteers, great fun!<br />
:'''2009-05-21''': [[Five Minutes of Fame]]<br />
:'''2009-04-27''': [[EagleCAD workshop]] -- learn to use this CAD tool for printed circuit board design<br />
:'''2009-04-16''': [[Five Minutes of Fame]] April showers &amp; flowers edition<br />
:'''2009-04-11''': [[RFID Hacking]] weekend workshop (this event moved from the original March date)<br />
:'''2009-04-05''': [[First aid and CPR class]] Learning how to not only not die, but also reduce scarring!<br />
:'''2009-04-03''': [[Sudo pop]] 2PM and on. Making the first batch of a Noisebridge label yerba mate-niated rootbrew, gratis and DIY<br />
:'''2009-03-26''': [[OpenEEG | OpenEEG Hacking]] first meet up for this new group: 8 pm<br />
:'''2009-03-19''': [[Five Minutes of Fame]]<br />
:'''2009-03-12''': [[OpenBTS and GSM]] talk by David Burgess<br />
:'''2009-02-14''': [[Open Heart Workshop]] Valentine's Day blinkyheart soldering party! <br />
:'''2009-02-13''': [[Time-t_Party|&lt;tt&gt;time_t&lt;/tt&gt; Party]] to celebrate 1,234,567,890 since the Unix epoch.<br />
:'''2009-02-09''': [[Spanish learning at 8:30]]<br />
:'''2009-02-05''': [[PGP Key Workshop]]<br />
:'''2009-01-31''': [[Locksport and Lockpicking]]<br />
<br />
===2008===<br />
:'''2008-12-27''': [[25C3]] Chaos Computer Congress in Berlin<br />
:'''2008-12-20 &amp; 21''': [[Creme Brulee]] Workshop on creating a french dessert, with bonus propane torch.<br />
:'''2008-12-17 20:00''': [[Machine Learning]] Birds-of-a-feather<br />
:'''2008-11-24''': [[Circuit Hacking Monday]] circuit design workshop<br />
:'''2008-11-21, 7pm''':[[Milk and Cookies]] -- [[User:Dmolnar|David Molnar]] hosts Milk and Cookies at 83C. Bring a short 5-7minute thing to read to others. Bring a potluck cookie/snack/drink if you like. David will bring milk and cookies.<br />
:'''2008-11-17, 7:30pm''': [[Basic Bicycle Maintain]] - [[User:rubin110|Rubin]] and [[User:rigel|rigel]] hate it when we see a bike that isn't maintained. Screechy chains and clacking derailleur can go to hell. Basic bike tune up, sharing the smarts on simple things you can do at home to make your ride suck a whole lot less.<br />
:'''2008-11-16, 5:00pm''': [[RepRap Soldering Party]] - help assemble RepRap! RSVPs required on wiki! [[User:Adi|adi]]<br />
:'''2008-11-16, 3:00pm''': [[Oscilloscopes]] - Learn how to use this versatile tool to test electronic circuits. Maximum 6 slots, please sign up ahead of time! [[User:dstaff|dstaff]]<br />
:'''2008-10-31''': [[Halloween Open House]] - NoiseBridge's own [[PPPC]] threw an awesome open house/halloween gala. Post pictures if you got 'em!<br />
:'''2008-10-25''': [[Soldering Workshop]] and Pumpkin Hackin' - Learn to solder for total newbies (or learn to solder better!), including surface mount. Additionally, carve your halloween pumpkins and enjoy some experimental pumpkin pie and/or soup.<br />
:'''2008-10-07''': (tuesday before meeting) - Etch a circuit board. I'll be trying a photo resist etching and a basic printed mask etching. This is step 1/3 for a project called &quot;annoying USB thingie&quot; which will execute pre-defined keystrokes by sneaking a tiny USB dongle onto a victim^h^h^h^h^h buddy's computer.<br />
:'''2008-09-13''': [[Processing Workshop]] — Learn this very easy-to-use programming language! - [[Processing Workshop Report]]<br />
:'''2008-02-16''': [[Brain Machine Workshop|Brain Machine Making Workshop]]: Our first hardware sprint!</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T06:53:21Z<p>Turbclnt: </p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the Mount===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
[[File:2011-04-17_18.22.36.jpg|300px|center]]<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|center]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
[[File:2011-04-19_21.47.13.jpg|300px|center]]<br />
<br />
'''Step 4:''' Get out your CPVC fittings and cut 2x ~3&quot; length from your 1/2&quot; CPVC pipe. Prime, then cement these fittings together in a zigzag shape (think tetris) to act as a light trap. Cement one side to a coupler. The below drawing should help with the description:<br />
<br />
[[File:Pipe_Diagram.jpg|center]]<br />
<br />
'''Step 5:''' Attach the remaining 1/2&quot; coupler to one side of the 1/2&quot; CPVC pipe<br />
<br />
===Make the Film===<br />
<br />
'''Step 1:''' Dissolve your Ru(dppf) complex in ~1mL acetone (nail polish remover). '''Do not attempt to take the Ru(dppf) complex out of the bottle!!''' There is such a tiny amount in the bottle that you will surely lose a fair amount due to handling. Instead, add the acetone directly to the bottle the compound was shipped in, and confirm it dissolves. You should have a very bright orange solution without any particles in it. Using an eyedropper or something similar for this step will help ''immensely''.<br />
<br />
'''Step 2:''' Cut a ~1.5&quot;x1.5&quot; square of mylar filmfrom your stock mylar sheet using scissors.<br />
<br />
'''Step 3:''' Using a hot glue gun, lay down a hot glue &quot;circle&quot; that is approximately 0.5&quot; in diameter. This will act as a dam to prevent your acetone/Ru(dppf) mixture from spreading all over the film.<br />
<br />
'''Step 4:''' Using an eyedropper, deposit ~1/5th of the amount of solution made in step 1 into the center of the circle. Allow this to dry uncovered until you can't see any solvent remaining. Overnight is not a bad idea. '''Do not use heat'''. Heat will not only cause the mylar film to distort, but it will also destroy the Ru(dppf) complex thus making it non-fluorescent! Do like your mom always told you and be patient. When you are done, you should have a film that looks something like the film on the right. The other films show what happens if you try to rush things. Note the hazy centers! You want a bright, non-hazy layer ideally:<br />
<br />
[[File:2011-04-19_20.30.33.jpg|300px|center]]<br />
<br />
'''Learning and Important Information:''' This part of the project did not go so well. Trying to creating a uniform film in this manner is not a good idea as you can see in the pictures. In fact, due to the non-uniformity of the film, no reliable sensor measurement could be obtained :(. Several other ways of producing a thin film were attempted including:<br />
* Using a galvanized washer as a barrier instead so it could be removed (surface tension pulled the solution under the washer instead)<br />
* Using no barrier at all (the film became too thin to fluoresce)<br />
* Using 2 aluminum plates pressed on both sides to produce a thin film (the film became too thin to fluoresce in this situation too)<br />
* Constantly moving the mylar sheet to prevent movement of the solvent to the outside (there is no overcoming surface tension! This just didn't work)<br />
* '''Suggestions on solving this difficult problem would be desired!''' [http://www.tciinc.com/coating.html Knife coating, or some other de-facto coating mechanism] is an option I considered here, but it would also require some specialized equipment that isn't available to everyone.<br />
<br />
'''Step 5:''' After you are convinced the nail polish remover has evaporated, seal the top of the film (non-mylar side) with the vinyl glue. This prevents oxygen from reaching the reverse side of the optode film.<br />
<br />
'''Step 6:''' Lastly, mount the film in the 3/4&quot; compression housing. The film should sit over a coupler, with the mylar side facing the experiment. Pull the o-ring down over the sides of the film to create a waterproof barrier for the circuitry, then insert the coupler into the 3/4&quot; compression housing (even though the sizes are mismatched, these fit together quite nicely, and are waterproof due to the rubber o-rings.<br />
<br />
[[File:2011-04-19_20.29.22.jpg|300px|center]]<br />
<br />
===Build the Circuit===<br />
<br />
Design the following circuit on a breadboard or a protoboard of your choice (note: arduino pin assignments can be changed, but the code is setup to use those listed by default):<br />
<br />
[[File:Circuit_diagram.jpg|center]]<br />
<br />
Arduino code to blink the LED and read from the phototransistor is available here. A-D values are printed to the serial monitor in this implementation.<br />
<br />
===Assemble Everything===<br />
<br />
Make sure everything is working like it is supposed to - does the LED turn on? Does it illuminate the film? If it is all working, slide it into the the compression fitting (see the orange?? COOOOL!)<br />
<br />
[[File:2011-04-19_20.37.33.jpg|600px|center]]<br />
<br />
After the mount is in place, screw both ends of the compression fitting on, and you've got a light proof, waterproof mount!<br />
<br />
[[File:Assembled.jpg|center]]<br />
<br />
=Making it cooler=<br />
<br />
So, I do need to bring this up one more time: '''This optode did not work'''. I'm 90% sure it had to do with not being able to produce a film of uniform coverage in a reliable manner. Suggestions here are welcomed! So, undoubtedly, this would be the way to make it waaaaay cooler. <br />
<br />
In addition, this probe was not made with any type of calibration, so it would only be useful for tracking relative changes in dissolved oxygen in a single system. Adding a calibrated system to the arduino code would make results transferable probe to probe. <br />
<br />
=Geeking out=<br />
<br />
There is more than 1 way to use fluorescence to measure oxygen. Instead of using intensity of light produced (easiest to implement, but hardest to calibrate), you could instead measure the decay rate - i.e. the amount of time it takes for the film to go from illuminated to non-illuminated in the presence of no light. If you couple this with a '''red''' LED (which the film will not absorb), you have an internal standard that need not be calibrated for a very, very long time. Awesome! The problem is, this decay rate is very fast - on the nanosecond order, so the backend electronics would need to be more sophisticated. In addition, the red LED would likely not be properly filtered out by the phototransistor, thus requiring the need for a bandpass filter, raising complexity and cost.<br />
<br />
=Links=<br />
* I promise people have gotten this to work - [http://www.pco.de/fileadmin/user_upload/db/download/GHoBGr_SAB74_78_90.pdf check this out!]</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T06:44:57Z<p>Turbclnt: /* Assemble Everything */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the Mount===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
[[File:2011-04-17_18.22.36.jpg|300px|center]]<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|center]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
[[File:2011-04-19_21.47.13.jpg|300px|center]]<br />
<br />
'''Step 4:''' Get out your CPVC fittings and cut 2x ~3&quot; length from your 1/2&quot; CPVC pipe. Prime, then cement these fittings together in a zigzag shape (think tetris) to act as a light trap. Cement one side to a coupler. The below drawing should help with the description:<br />
<br />
[[File:Pipe_Diagram.jpg|center]]<br />
<br />
'''Step 5:''' Attach the remaining 1/2&quot; coupler to one side of the 1/2&quot; CPVC pipe<br />
<br />
===Make the Film===<br />
<br />
'''Step 1:''' Dissolve your Ru(dppf) complex in ~1mL acetone (nail polish remover). '''Do not attempt to take the Ru(dppf) complex out of the bottle!!''' There is such a tiny amount in the bottle that you will surely lose a fair amount due to handling. Instead, add the acetone directly to the bottle the compound was shipped in, and confirm it dissolves. You should have a very bright orange solution without any particles in it. Using an eyedropper or something similar for this step will help ''immensely''.<br />
<br />
'''Step 2:''' Cut a ~1.5&quot;x1.5&quot; square of mylar filmfrom your stock mylar sheet using scissors.<br />
<br />
'''Step 3:''' Using a hot glue gun, lay down a hot glue &quot;circle&quot; that is approximately 0.5&quot; in diameter. This will act as a dam to prevent your acetone/Ru(dppf) mixture from spreading all over the film.<br />
<br />
'''Step 4:''' Using an eyedropper, deposit ~1/5th of the amount of solution made in step 1 into the center of the circle. Allow this to dry uncovered until you can't see any solvent remaining. Overnight is not a bad idea. '''Do not use heat'''. Heat will not only cause the mylar film to distort, but it will also destroy the Ru(dppf) complex thus making it non-fluorescent! Do like your mom always told you and be patient. When you are done, you should have a film that looks something like the film on the right. The other films show what happens if you try to rush things. Note the hazy centers! You want a bright, non-hazy layer ideally:<br />
<br />
[[File:2011-04-19_20.30.33.jpg|300px|center]]<br />
<br />
'''Learning and Important Information:''' This part of the project did not go so well. Trying to creating a uniform film in this manner is not a good idea as you can see in the pictures. In fact, due to the non-uniformity of the film, no reliable sensor measurement could be obtained :(. Several other ways of producing a thin film were attempted including:<br />
* Using a galvanized washer as a barrier instead so it could be removed (surface tension pulled the solution under the washer instead)<br />
* Using no barrier at all (the film became too thin to fluoresce)<br />
* Using 2 aluminum plates pressed on both sides to produce a thin film (the film became too thin to fluoresce in this situation too)<br />
* Constantly moving the mylar sheet to prevent movement of the solvent to the outside (there is no overcoming surface tension! This just didn't work)<br />
* '''Suggestions on solving this difficult problem would be desired!''' [http://www.tciinc.com/coating.html Knife coating, or some other de-facto coating mechanism] is an option I considered here, but it would also require some specialized equipment that isn't available to everyone.<br />
<br />
'''Step 5:''' After you are convinced the nail polish remover has evaporated, seal the top of the film (non-mylar side) with the vinyl glue. This prevents oxygen from reaching the reverse side of the optode film.<br />
<br />
'''Step 6:''' Lastly, mount the film in the 3/4&quot; compression housing. The film should sit over a coupler, with the mylar side facing the experiment. Pull the o-ring down over the sides of the film to create a waterproof barrier for the circuitry, then insert the coupler into the 3/4&quot; compression housing (even though the sizes are mismatched, these fit together quite nicely, and are waterproof due to the rubber o-rings.<br />
<br />
[[File:2011-04-19_20.29.22.jpg|300px|center]]<br />
<br />
===Build the Circuit===<br />
<br />
Design the following circuit on a breadboard or a protoboard of your choice (note: arduino pin assignments can be changed, but the code is setup to use those listed by default):<br />
<br />
[[File:Circuit_diagram.jpg|center]]<br />
<br />
Arduino code to blink the LED and read from the phototransistor is available here. A-D values are printed to the serial monitor in this implementation.<br />
<br />
===Assemble Everything===<br />
<br />
Make sure everything is working like it is supposed to - does the LED turn on? Does it illuminate the film? If it is all working, slide it into the the compression fitting (see the orange?? COOOOL!)<br />
<br />
[[File:2011-04-19_20.37.33.jpg|600px|center]]<br />
<br />
After the mount is in place, screw both ends of the compression fitting on, and you've got a light proof, waterproof mount!<br />
<br />
[[File:Assembled.jpg|center]]<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T06:44:32Z<p>Turbclnt: /* How to build it */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the Mount===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
[[File:2011-04-17_18.22.36.jpg|300px|center]]<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|center]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
[[File:2011-04-19_21.47.13.jpg|300px|center]]<br />
<br />
'''Step 4:''' Get out your CPVC fittings and cut 2x ~3&quot; length from your 1/2&quot; CPVC pipe. Prime, then cement these fittings together in a zigzag shape (think tetris) to act as a light trap. Cement one side to a coupler. The below drawing should help with the description:<br />
<br />
[[File:Pipe_Diagram.jpg|center]]<br />
<br />
'''Step 5:''' Attach the remaining 1/2&quot; coupler to one side of the 1/2&quot; CPVC pipe<br />
<br />
===Make the Film===<br />
<br />
'''Step 1:''' Dissolve your Ru(dppf) complex in ~1mL acetone (nail polish remover). '''Do not attempt to take the Ru(dppf) complex out of the bottle!!''' There is such a tiny amount in the bottle that you will surely lose a fair amount due to handling. Instead, add the acetone directly to the bottle the compound was shipped in, and confirm it dissolves. You should have a very bright orange solution without any particles in it. Using an eyedropper or something similar for this step will help ''immensely''.<br />
<br />
'''Step 2:''' Cut a ~1.5&quot;x1.5&quot; square of mylar filmfrom your stock mylar sheet using scissors.<br />
<br />
'''Step 3:''' Using a hot glue gun, lay down a hot glue &quot;circle&quot; that is approximately 0.5&quot; in diameter. This will act as a dam to prevent your acetone/Ru(dppf) mixture from spreading all over the film.<br />
<br />
'''Step 4:''' Using an eyedropper, deposit ~1/5th of the amount of solution made in step 1 into the center of the circle. Allow this to dry uncovered until you can't see any solvent remaining. Overnight is not a bad idea. '''Do not use heat'''. Heat will not only cause the mylar film to distort, but it will also destroy the Ru(dppf) complex thus making it non-fluorescent! Do like your mom always told you and be patient. When you are done, you should have a film that looks something like the film on the right. The other films show what happens if you try to rush things. Note the hazy centers! You want a bright, non-hazy layer ideally:<br />
<br />
[[File:2011-04-19_20.30.33.jpg|300px|center]]<br />
<br />
'''Learning and Important Information:''' This part of the project did not go so well. Trying to creating a uniform film in this manner is not a good idea as you can see in the pictures. In fact, due to the non-uniformity of the film, no reliable sensor measurement could be obtained :(. Several other ways of producing a thin film were attempted including:<br />
* Using a galvanized washer as a barrier instead so it could be removed (surface tension pulled the solution under the washer instead)<br />
* Using no barrier at all (the film became too thin to fluoresce)<br />
* Using 2 aluminum plates pressed on both sides to produce a thin film (the film became too thin to fluoresce in this situation too)<br />
* Constantly moving the mylar sheet to prevent movement of the solvent to the outside (there is no overcoming surface tension! This just didn't work)<br />
* '''Suggestions on solving this difficult problem would be desired!''' [http://www.tciinc.com/coating.html Knife coating, or some other de-facto coating mechanism] is an option I considered here, but it would also require some specialized equipment that isn't available to everyone.<br />
<br />
'''Step 5:''' After you are convinced the nail polish remover has evaporated, seal the top of the film (non-mylar side) with the vinyl glue. This prevents oxygen from reaching the reverse side of the optode film.<br />
<br />
'''Step 6:''' Lastly, mount the film in the 3/4&quot; compression housing. The film should sit over a coupler, with the mylar side facing the experiment. Pull the o-ring down over the sides of the film to create a waterproof barrier for the circuitry, then insert the coupler into the 3/4&quot; compression housing (even though the sizes are mismatched, these fit together quite nicely, and are waterproof due to the rubber o-rings.<br />
<br />
[[File:2011-04-19_20.29.22.jpg|300px|center]]<br />
<br />
===Build the Circuit===<br />
<br />
Design the following circuit on a breadboard or a protoboard of your choice (note: arduino pin assignments can be changed, but the code is setup to use those listed by default):<br />
<br />
[[File:Circuit_diagram.jpg|center]]<br />
<br />
Arduino code to blink the LED and read from the phototransistor is available here. A-D values are printed to the serial monitor in this implementation.<br />
<br />
===Assemble Everything===<br />
<br />
Make sure everything is working like it is supposed to - does the LED turn on? Does it illuminate the film? If it is all working, slide it into the the compression fitting (see the orange?? COOOOL!)<br />
<br />
[[File:2011-04-19_20.37.33.jpg|center]]<br />
<br />
After the mount is in place, screw both ends of the compression fitting on, and you've got a light proof, waterproof mount!<br />
<br />
[[File:Assembled.jpg|center]]<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/File:Assembled.jpgFile:Assembled.jpg2011-05-04T06:44:07Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/File:2011-04-19_20.37.33.jpgFile:2011-04-19 20.37.33.jpg2011-05-04T06:42:34Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T06:36:54Z<p>Turbclnt: /* How to build it */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the Mount===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
[[File:2011-04-17_18.22.36.jpg|300px|center]]<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|center]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
[[File:2011-04-19_21.47.13.jpg|300px|center]]<br />
<br />
'''Step 4:''' Get out your CPVC fittings and cut 2x ~3&quot; length from your 1/2&quot; CPVC pipe. Prime, then cement these fittings together in a zigzag shape (think tetris) to act as a light trap. Cement one side to a coupler. The below drawing should help with the description:<br />
<br />
[[File:Pipe_Diagram.jpg|center]]<br />
<br />
'''Step 5:''' Attach the remaining 1/2&quot; coupler to one side of the 1/2&quot; CPVC pipe<br />
<br />
===Make the Film===<br />
<br />
'''Step 1:''' Dissolve your Ru(dppf) complex in ~1mL acetone (nail polish remover). '''Do not attempt to take the Ru(dppf) complex out of the bottle!!''' There is such a tiny amount in the bottle that you will surely lose a fair amount due to handling. Instead, add the acetone directly to the bottle the compound was shipped in, and confirm it dissolves. You should have a very bright orange solution without any particles in it. Using an eyedropper or something similar for this step will help ''immensely''.<br />
<br />
'''Step 2:''' Cut a ~1.5&quot;x1.5&quot; square of mylar filmfrom your stock mylar sheet using scissors.<br />
<br />
'''Step 3:''' Using a hot glue gun, lay down a hot glue &quot;circle&quot; that is approximately 0.5&quot; in diameter. This will act as a dam to prevent your acetone/Ru(dppf) mixture from spreading all over the film.<br />
<br />
'''Step 4:''' Using an eyedropper, deposit ~1/5th of the amount of solution made in step 1 into the center of the circle. Allow this to dry uncovered until you can't see any solvent remaining. Overnight is not a bad idea. '''Do not use heat'''. Heat will not only cause the mylar film to distort, but it will also destroy the Ru(dppf) complex thus making it non-fluorescent! Do like your mom always told you and be patient. When you are done, you should have a film that looks something like the film on the right. The other films show what happens if you try to rush things. Note the hazy centers! You want a bright, non-hazy layer ideally:<br />
<br />
[[File:2011-04-19_20.30.33.jpg|300px|center]]<br />
<br />
'''Learning and Important Information:''' This part of the project did not go so well. Trying to creating a uniform film in this manner is not a good idea as you can see in the pictures. In fact, due to the non-uniformity of the film, no reliable sensor measurement could be obtained :(. Several other ways of producing a thin film were attempted including:<br />
* Using a galvanized washer as a barrier instead so it could be removed (surface tension pulled the solution under the washer instead)<br />
* Using no barrier at all (the film became too thin to fluoresce)<br />
* Using 2 aluminum plates pressed on both sides to produce a thin film (the film became too thin to fluoresce in this situation too)<br />
* Constantly moving the mylar sheet to prevent movement of the solvent to the outside (there is no overcoming surface tension! This just didn't work)<br />
* '''Suggestions on solving this difficult problem would be desired!''' [http://www.tciinc.com/coating.html Knife coating, or some other de-facto coating mechanism] is an option I considered here, but it would also require some specialized equipment that isn't available to everyone.<br />
<br />
'''Step 5:''' After you are convinced the nail polish remover has evaporated, seal the top of the film (non-mylar side) with the vinyl glue. This prevents oxygen from reaching the reverse side of the optode film.<br />
<br />
'''Step 6:''' Lastly, mount the film in the 3/4&quot; compression housing. The film should sit over a coupler, with the mylar side facing the experiment. Pull the o-ring down over the sides of the film to create a waterproof barrier for the circuitry, then insert the coupler into the 3/4&quot; compression housing (even though the sizes are mismatched, these fit together quite nicely, and are waterproof due to the rubber o-rings.<br />
<br />
[[File:2011-04-19_20.29.22.jpg|300px|center]]<br />
<br />
===Build the Circuit===<br />
<br />
Design the following circuit on a breadboard or a protoboard of your choice (note: arduino pin assignments can be changed, but the code is setup to use those listed by default):<br />
<br />
[[File:Circuit_diagram.jpg|center]]<br />
<br />
Arduino code to blink the LED and read from the phototransistor is available here<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/File:Circuit_diagram.jpgFile:Circuit diagram.jpg2011-05-04T06:35:50Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T06:26:00Z<p>Turbclnt: /* Make the Film */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the Mount===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
[[File:2011-04-17_18.22.36.jpg|300px|center]]<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|center]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
[[File:2011-04-19_21.47.13.jpg|300px|center]]<br />
<br />
'''Step 4:''' Get out your CPVC fittings and cut 2x ~3&quot; length from your 1/2&quot; CPVC pipe. Prime, then cement these fittings together in a zigzag shape (think tetris) to act as a light trap. Cement one side to a coupler. The below drawing should help with the description:<br />
<br />
[[File:Pipe_Diagram.jpg|center]]<br />
<br />
'''Step 5:''' Attach the remaining 1/2&quot; coupler to one side of the 1/2&quot; CPVC pipe<br />
<br />
===Make the Film===<br />
<br />
'''Step 1:''' Dissolve your Ru(dppf) complex in ~1mL acetone (nail polish remover). '''Do not attempt to take the Ru(dppf) complex out of the bottle!!''' There is such a tiny amount in the bottle that you will surely lose a fair amount due to handling. Instead, add the acetone directly to the bottle the compound was shipped in, and confirm it dissolves. You should have a very bright orange solution without any particles in it. Using an eyedropper or something similar for this step will help ''immensely''.<br />
<br />
'''Step 2:''' Cut a ~1.5&quot;x1.5&quot; square of mylar filmfrom your stock mylar sheet using scissors.<br />
<br />
'''Step 3:''' Using a hot glue gun, lay down a hot glue &quot;circle&quot; that is approximately 0.5&quot; in diameter. This will act as a dam to prevent your acetone/Ru(dppf) mixture from spreading all over the film.<br />
<br />
'''Step 4:''' Using an eyedropper, deposit ~1/5th of the amount of solution made in step 1 into the center of the circle. Allow this to dry uncovered until you can't see any solvent remaining. Overnight is not a bad idea. '''Do not use heat'''. Heat will not only cause the mylar film to distort, but it will also destroy the Ru(dppf) complex thus making it non-fluorescent! Do like your mom always told you and be patient. When you are done, you should have a film that looks something like the film on the right. The other films show what happens if you try to rush things. Note the hazy centers! You want a bright, non-hazy layer ideally:<br />
<br />
[[File:2011-04-19_20.30.33.jpg|300px|center]]<br />
<br />
'''Learning and Important Information:''' This part of the project did not go so well. Trying to creating a uniform film in this manner is not a good idea as you can see in the pictures. In fact, due to the non-uniformity of the film, no reliable sensor measurement could be obtained :(. Several other ways of producing a thin film were attempted including:<br />
* Using a galvanized washer as a barrier instead so it could be removed (surface tension pulled the solution under the washer instead)<br />
* Using no barrier at all (the film became too thin to fluoresce)<br />
* Using 2 aluminum plates pressed on both sides to produce a thin film (the film became too thin to fluoresce in this situation too)<br />
* Constantly moving the mylar sheet to prevent movement of the solvent to the outside (there is no overcoming surface tension! This just didn't work)<br />
* '''Suggestions on solving this difficult problem would be desired!''' [http://www.tciinc.com/coating.html Knife coating, or some other de-facto coating mechanism] is an option I considered here, but it would also require some specialized equipment that isn't available to everyone.<br />
<br />
'''Step 5:''' After you are convinced the nail polish remover has evaporated, seal the top of the film (non-mylar side) with the vinyl glue. This prevents oxygen from reaching the reverse side of the optode film.<br />
<br />
'''Step 6:''' Lastly, mount the film in the 3/4&quot; compression housing. The film should sit over a coupler, with the mylar side facing the experiment. Pull the o-ring down over the sides of the film to create a waterproof barrier for the circuitry, then insert the coupler into the 3/4&quot; compression housing (even though the sizes are mismatched, these fit together quite nicely, and are waterproof due to the rubber o-rings.<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/File:2011-04-19_20.29.22.jpgFile:2011-04-19 20.29.22.jpg2011-05-04T06:25:51Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T06:21:49Z<p>Turbclnt: /* Make the Film */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the Mount===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
[[File:2011-04-17_18.22.36.jpg|300px|center]]<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|center]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
[[File:2011-04-19_21.47.13.jpg|300px|center]]<br />
<br />
'''Step 4:''' Get out your CPVC fittings and cut 2x ~3&quot; length from your 1/2&quot; CPVC pipe. Prime, then cement these fittings together in a zigzag shape (think tetris) to act as a light trap. Cement one side to a coupler. The below drawing should help with the description:<br />
<br />
[[File:Pipe_Diagram.jpg|center]]<br />
<br />
'''Step 5:''' Attach the remaining 1/2&quot; coupler to one side of the 1/2&quot; CPVC pipe<br />
<br />
===Make the Film===<br />
<br />
'''Step 1:''' Dissolve your Ru(dppf) complex in ~1mL acetone (nail polish remover). '''Do not attempt to take the Ru(dppf) complex out of the bottle!!''' There is such a tiny amount in the bottle that you will surely lose a fair amount due to handling. Instead, add the acetone directly to the bottle the compound was shipped in, and confirm it dissolves. You should have a very bright orange solution without any particles in it. Using an eyedropper or something similar for this step will help ''immensely''.<br />
<br />
'''Step 2:''' Cut a ~1.5&quot;x1.5&quot; square of mylar filmfrom your stock mylar sheet using scissors.<br />
<br />
'''Step 3:''' Using a hot glue gun, lay down a hot glue &quot;circle&quot; that is approximately 0.5&quot; in diameter. This will act as a dam to prevent your acetone/Ru(dppf) mixture from spreading all over the film.<br />
<br />
'''Step 4:''' Using an eyedropper, deposit ~1/5th of the amount of solution made in step 1 into the center of the circle. Allow this to dry uncovered until you can't see any solvent remaining. Overnight is not a bad idea. '''Do not use heat'''. Heat will not only cause the mylar film to distort, but it will also destroy the Ru(dppf) complex thus making it non-fluorescent! Do like your mom always told you and be patient. When you are done, you should have a film that looks something like the film on the right. The other films show what happens if you try to rush things. Note the hazy centers! You want a bright, non-hazy layer ideally:<br />
<br />
[[File:2011-04-19_20.30.33.jpg|300px|center]]<br />
<br />
'''Learning and Important Information:''' This part of the project did not go so well. Trying to creating a uniform film in this manner is not a good idea as you can see in the pictures. In fact, due to the non-uniformity of the film, no reliable sensor measurement could be obtained :(. Several other ways of producing a thin film were attempted including:<br />
* Using a galvanized washer as a barrier instead so it could be removed (surface tension pulled the solution under the washer instead)<br />
* Using no barrier at all (the film became too thin to fluoresce)<br />
* Using 2 aluminum plates pressed on both sides to produce a thin film (the film became too thin to fluoresce in this situation too)<br />
* Constantly moving the mylar sheet to prevent movement of the solvent to the outside (there is no overcoming surface tension! This just didn't work)<br />
* '''Suggestions on solving this difficult problem would be desired!''' [http://www.tciinc.com/coating.html Knife coating, or some other de-facto coating mechanism] is an option I considered here, but it would also require some specialized equipment that isn't available to everyone.<br />
<br />
'''Step 5:''' After you are convinced the nail polish remover has evaporated, seal the top of the film (non-mylar side) with the vinyl glue. This prevents oxygen from reaching the reverse side of the optode film.<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T06:20:37Z<p>Turbclnt: /* Build the LED and Phototransistor Brackets */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the Mount===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
[[File:2011-04-17_18.22.36.jpg|300px|center]]<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|center]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
[[File:2011-04-19_21.47.13.jpg|300px|center]]<br />
<br />
'''Step 4:''' Get out your CPVC fittings and cut 2x ~3&quot; length from your 1/2&quot; CPVC pipe. Prime, then cement these fittings together in a zigzag shape (think tetris) to act as a light trap. Cement one side to a coupler. The below drawing should help with the description:<br />
<br />
[[File:Pipe_Diagram.jpg|center]]<br />
<br />
'''Step 5:''' Attach the remaining 1/2&quot; coupler to one side of the 1/2&quot; CPVC pipe<br />
<br />
===Make the Film===<br />
<br />
'''Step 1:''' Dissolve your Ru(dppf) complex in ~1mL acetone (nail polish remover). '''Do not attempt to take the Ru(dppf) complex out of the bottle!!''' There is such a tiny amount in the bottle that you will surely lose a fair amount due to handling. Instead, add the acetone directly to the bottle the compound was shipped in, and confirm it dissolves. You should have a very bright orange solution without any particles in it. Using an eyedropper or something similar for this step will help ''immensely''.<br />
<br />
'''Step 2:''' Cut a ~1.5&quot;x1.5&quot; square of mylar filmfrom your stock mylar sheet using scissors.<br />
<br />
'''Step 3:''' Using a hot glue gun, lay down a hot glue &quot;circle&quot; that is approximately 0.5&quot; in diameter. This will act as a dam to prevent your acetone/Ru(dppf) mixture from spreading all over the film.<br />
<br />
'''Step 4:''' Using an eyedropper, deposit ~1/5th of the amount of solution made in step 1 into the center of the circle. Allow this to dry uncovered until you can't see any solvent remaining. Overnight is not a bad idea. '''Do not use heat'''. Heat will not only cause the mylar film to distort, but it will also destroy the Ru(dppf) complex thus making it non-fluorescent! Do like your mom always told you and be patient. When you are done, you should have a film that looks something like the film on the right. The other films show what happens if you try to rush things. Note the hazy centers! You want a bright, non-hazy layer ideally:<br />
<br />
[[File:2011-04-19_20.30.33.jpg|300px|center]]<br />
<br />
'''Learning and Important Information:''' This part of the project did not go so well. Trying to creating a uniform film in this manner is not a good idea as you can see in the pictures. In fact, due to the non-uniformity of the film, no reliable sensor readings could be determined. Several other ways of producing a thin film were attempted including:<br />
* Using a galvanized washer as a barrier instead so it could be removed (surface tension pulled the solution under the washer instead)<br />
* Using no barrier at all (the film became too thin to fluoresce)<br />
* Using 2 aluminum plates pressed on both sides to produce a thin film (the film became too thin to fluoresce in this situation too)<br />
* Constantly moving the mylar sheet to prevent movement of the solvent to the outside (there is no overcoming surface tension! This just didn't work)<br />
* '''Suggestions on solving this difficult problem would be desired!''' [http://www.tciinc.com/coating.html Knife coating, or some other de-facto coating mechanism] is an option I considered here, but it would also require some specialized equipment that isn't available to everyone.<br />
<br />
'''Step 5:''' After you are convinced the nail polish remover has evaporated, seal the top of the film (non-mylar side) with the vinyl glue. This prevents oxygen from reaching the reverse side of the optode film.<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/File:2011-04-19_20.30.33.jpgFile:2011-04-19 20.30.33.jpg2011-05-04T06:12:23Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/File:2011-04-19_21.47.13.jpgFile:2011-04-19 21.47.13.jpg2011-05-04T06:10:39Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/File:Pipe_Diagram.jpgFile:Pipe Diagram.jpg2011-05-04T05:59:54Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/File:2011-04-17_18.22.36.jpgFile:2011-04-17 18.22.36.jpg2011-05-04T05:51:31Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:49:54Z<p>Turbclnt: /* Build the LED and Phototransistor Brackets */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the LED and Phototransistor Brackets===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|center]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:49:35Z<p>Turbclnt: /* Build the LED and Phototransistor Brackets */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the LED and Phototransistor Brackets===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:49:01Z<p>Turbclnt: /* How to build it */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
===Build the LED and Phototransistor Brackets===<br />
<br />
'''Step 1:''' When you are done, these need to fit inside the 3/4&quot; CPVC compression coupling. These parts hold the LED and phototransistor needed to illuminate/measure the optode film. I decided to cut these pieces out of 3/4&quot; thick scrap wood on a scroll saw. I traced 0.875&quot; diameter circles onto a piece of wood, then got to work on a scroll saw:<br />
<br />
After sawing, I sanded down the edges to make the pieces pretty circles that fit snugly inside the 3/4&quot; compression coupling. At this point, you should have 2x 3/4&quot; diameter circles that fit snugly inside the 3/4&quot; compression coupling. Check to make sure this is true!<br />
<br />
'''Step 2:''' Using a drill press, I cut 1/16&quot; holes for the LED and phototransistor leads. Additionally, I cut a 1/4&quot; diameter hole to expose the phototransistor (which will sit below the blue LED). Note that holes do need to line up between layers, so using a drill press will make life easier. At this point, you should have something that looks like this:<br />
<br />
[[File:2011-04-19_21.45.47.jpg|300px|thumb]]<br />
<br />
'''Step 3:''' Insert the LED and phototransistor into the holes to makes sure there is a good fit, and all the leads stick out the bottom of your mount. If this all checks out, wood glue the two layers together, fixing the position of the blue LED and phototransistor. It is important that the phototransistor be attached on the bottom layer to filter out excess light coming from the blue LED.<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/File:2011-04-19_21.45.47.jpgFile:2011-04-19 21.45.47.jpg2011-05-04T05:46:27Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:32:44Z<p>Turbclnt: /* How to build it */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Safety and Hazard Stuff===<br />
* Acetone (nail polish remover) is a solvent. Don't play with it around fire. Try to play with it in a ventilated area.<br />
* The Ru(dppf) complex doesn't have any specific hazards associated with it, so you can throw it away in small quantities at home. It will stain everything it touches bright orange like crazy though - gloves and/or bad clothes are handy.<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:29:23Z<p>Turbclnt: /* How to build it */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
'''Total Projected Cost: $22.07''' (oh yeah...did I mention commercial probes cost in excess of $400?!<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:27:14Z<p>Turbclnt: /* List of Supplies and links for purchase */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
====Mount and Housing====<br />
* 2x ~0.5&quot; diameter circles of 0.75&quot; thick scrap wood (again...look in dumpsters).<br />
* [http://www.lowes.com/pd_23761-322-50105N_0__?productId=3132991&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC couplings ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_23755-322-50705N_0__?productId=3132983&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc 2x 1/2&quot; CPVC elbows ($0.19/ea = $0.38 total)]<br />
* [http://www.lowes.com/pd_1315-33599-P600CTS+3/4_0__?productId=3351970&amp;Ntt=cpvc&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%26page%3D2 1x 3/4&quot; CPVC compression coupling ($3.67)]<br />
* [http://www.lowes.com/pd_351125-1814-PVC+04005++0200_0__?productId=3341538&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D3 ~2 feet 1/2&quot; ID CPVC Pipe ($0.78)]<br />
* [http://www.lowes.com/pd_23781-138-307560_0__?productId=1067279&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Primer (~$1.00)]<br />
* [http://www.lowes.com/pd_23776-138-31128D_0__?productId=3133009&amp;Ntt=cpvc+pipe&amp;pl=1&amp;currentURL=%2Fpl__0__s%3FNtt%3Dcpvc%2Bpipe%26page%3D4 CPVC Cement (~$1.00)]<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:15:46Z<p>Turbclnt: /* Electronics and Control */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:15:21Z<p>Turbclnt: </p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
Below is a list of links to the suppliers needed to get all the parts to build your own! Cost is listed on a per sensor basis, although you may have to buy more than the listed amount of cash from one supplier to get started.<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; clear Mylar film (~$0.50)]<br />
* [http://www.tapplastics.com/shop/product.php?pid=282&amp; Clear Vinyl adhesive (~$0.50)]<br />
* [http://www.drugstore.com/products/prod.asp?pid=204211&amp;aid=337953&amp;aparam=supernail_pure_acetone_&amp;CAWELAID=253643578 Pure Acetone Nail Polish Remover (~$0.10)]<br />
<br />
====Electronics and Control====<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView 1x 470nm high intensity blue LED ($1.35)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView 1x 940nm phototransistor ($0.35)<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690865_-1 1x 1k ohm resistor ($0.03)]<br />
* [https://www.jameco.com/webapp/wcs/stores/servlet/Product_10001_10001_690620_-1 1x 100 ohm resistor ($0.03)]<br />
* ~2 feet of old telephone cable to make your life easier (look in dumpsters people...jeez)<br />
<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T05:00:02Z<p>Turbclnt: /* How to build it */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===List of Supplies and links for purchase===<br />
<br />
====Optode Film====<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 0.1 - 0.2mg Ruthenium(II)-dppf dichloride complex (~$12)]<br />
* [<br />
<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T04:53:14Z<p>Turbclnt: /* Light Sealing */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Water &amp; Light Sealing===<br />
<br />
Since this device operates in the visual light spectrum, it must be sealed from ambient light in order to ensure low signal noise. Additionally, since the sensor is designed to measure ''dissolved'' oxygen, it must also be able to be submerged in a fluid. Although both these goals could be easily accomplished by building a custom mount on a mill or lathe, it would also make the overall device much less transferable to those without access to these expensive pieces of machinery.<br />
<br />
Instead, I turned to the plumbing aisle of my local hardware store, and found enough elbows, o-rings, and PVC cement to make a water and light tight mounting structure for under $10 that can be assembled without any special tools or training! See details below in the build section.<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T04:04:36Z<p>Turbclnt: /* Background &amp; plans to overcome technical hurdles */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
We need to ensure that the Ru(dppf) complex only senses oxygen change from the side of the film that our experiment is on, not the side of the film that the LEDs are on. Although this may seem to be a difficult problem at first, thankfully there are many polymers which have vastly differing oxygen diffusion properties. Additionally, it is very common that polymers list a number known as an '''oxygen diffusion coefficient'''. For super extra credit, and if you wanna be a chemistry geek, you can figure out what this means mathematically by studying [http://en.wikipedia.org/wiki/Fick%27s_laws_of_diffusion Fick's law of diffusion]. However, a short explanation of this will suffice for our needs.<br />
<br />
The higher the value of the diffusion coefficient, the faster oxygen will move a certain distance. So, in order to block oxygen from getting to one side of the film, you want to use a film with a very small diffusion coefficient, and/or a thick layer of film. If you want to allow oxygen to easily transport through a film, use a thin film with a very high diffusion coefficient...simple as that!<br />
<br />
For our project, we ended up using a [http://www.tapplastics.com/shop/product.php?pid=255&amp; 0.002&quot; thick layer of mylar film ($1.90/foot)] as the oxygen permeable film, and sandwiched our Ru(dppf) film between the mylar film and a ~0.5cm thick layer of [http://www.tapplastics.com/shop/product.php?pid=282&amp; clear vinyl adhesive ($3/tube...but you don't need much)] as an oxygen barrier layer. Details on the construction of this film can be found below.<br />
<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T03:39:18Z<p>Turbclnt: /* Detecting Film Fluorescence */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each. Additionally, because infrared is such a popular frequency for use in remote controls, it is very simple to find [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=2129385&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRTqBk%2BkkpQkP5cUrOGtVroxU6YZBPudcp3dbrpMUiCefI%2BF1soGN%2BJxhq%2BRpqPPJ1ZoV%0D%0AFrcEIwjsUIfq326mVTwP&amp;ddkey=http:StoreCatalogDrillDownView phototransistors that are very sensitive to light near 940nm] for only $0.35!<br />
<br />
A phototransistor varies the amount of current flowing through the collector/emitter junction based on the amount of light impacting on the phototransistor's light sensing surface. The amount of current produced can very simply, and reliably be read by a using a voltage divider circuit plugged into one of our Arduino's A-D converters. Additionally, if we take a quick peek at the [https://www.jameco.com/Jameco/Products/ProdDS/2129385.pdf datasheet for the mentioned phototransistor], we can see that the listed phototransistor is extremely insensitive to light emitting at wavelengths lower than 500nm. Therefore, with a proper LED mount design, it may be possible to detect the orange light given off by the Ru(dppf) film without having to implement an optical filter...neato!<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
Now that a material has been selected to <br />
<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T03:28:44Z<p>Turbclnt: /* Background &amp; plans to overcome technical hurdles */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each.<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
Now that a material has been selected to <br />
<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T03:28:16Z<p>Turbclnt: /* Detecting Film Fluorescence */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg|left]]<br />
<br />
The graph to the left is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each.<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
Now that a material has been selected to <br />
<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T03:27:33Z<p>Turbclnt: /* Detecting Film Fluorescence */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]:<br />
<br />
[[File:Emission_spectra.jpg]]<br />
<br />
The above graph is showing us two very valuable pieces of information. The curve near the left part of the graph is the '''absorbance curve'''. The higher this curve travels on the y-axis, the more light is absorbed by the Ru(dppf). When Ru(dppf) absorbs light, it immediately re-radiates it at a different color. The color that the Ru(dppf) emits is given in the right hand part of the graph known as the '''emission curve'''. Note that it does not emit a single wavelength of light - instead it is a range starting at ~550nm, and extending into the infrared spectrum.<br />
<br />
What does it all mean? What this graph means is that if we can illuminate our Ru(dppf) film with a bright light which has a wavelength near 455nm, our film will respond by emitting quite a bit of light ranging from 550nm (orange) - infrared. Cool! If we take a quick peek into our electronics catalogue, we quickly find several [https://www.jameco.com/webapp/wcs/stores/servlet/ProductDisplay?langId=-1&amp;productId=183222&amp;catalogId=10001&amp;storeId=10001&amp;krypto=9x3mj8umRToaOz4yqTl5KMcaoCI%2FfJNSYLR3XF4hfKZueAS%2FZKLb98U9IC6Z0qmaW9CKOQTSyrxY%0D%0ALa49x33gIumELMY5SLfQ&amp;ddkey=https:StoreCatalogDrillDownView high intensity blue LEDs with 470nm wavelengths] for $1.40/each.<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
Now that a material has been selected to <br />
<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/File:Emission_spectra.jpgFile:Emission spectra.jpg2011-05-04T03:15:31Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T03:13:24Z<p>Turbclnt: /* Plan to overcome technical hurdles */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Background &amp; plans to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
===Detecting Film Fluorescence===<br />
<br />
Now that we have identified a film material which we know will change color when exposed to varying oxygen levels, how will we be able to detect its change in color? Thankfully, the optical properties of Ru(dppf) are very well known and the manufacturer is very happy to provide technical information on their [http://www.sigmaaldrich.com/etc/medialib/docs/Fluka/Datasheet/76886dat.Par.0001.File.tmp/76886dat.pdf data sheet]<br />
<br />
<br />
===Film Permeability to Atmosphere===<br />
<br />
Now that a material has been selected to <br />
<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T03:06:24Z<p>Turbclnt: /* Flourescent Film Material */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Plan to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi 76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
<br />
<br />
<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T03:05:02Z<p>Turbclnt: /* Sensor Film Material */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Plan to overcome technical hurdles==<br />
<br />
===Flourescent Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we found the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
Our particular part is product number [&quot;http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=76886|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPECi&quot;|76886 from Sigma-Aldrich], which at the time of this writing was selling for $59/mg. Yes. You read that correctly - per milligram! If this material is so expensive? How do we expect to make a dO sensor for cheap? Thankfully, we don't need much of it...1mg was enough for us to make 5-6 films to test, thus bringing the price of this chemical to only $10 - $12 per film. Not too bad when you consider a commercial probe costs in the $400 range!<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
<br />
<br />
<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T02:59:15Z<p>Turbclnt: /* Sensor Film Material */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Plan to overcome technical hurdles==<br />
<br />
===Sensor Film Material===<br />
<br />
[[File:Rudppf.gif|frame|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we foudn the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
<br />
<br />
<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T02:58:05Z<p>Turbclnt: /* Sensor Film Material */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Plan to overcome technical hurdles==<br />
<br />
===Sensor Film Material===<br />
<br />
[[File:Rudppf.gif|right|Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II) dichloride complex which changes color based on amount of oxygen present]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we foudn the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
<br />
<br />
<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T02:56:10Z<p>Turbclnt: /* Sensor Film Material */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Plan to overcome technical hurdles==<br />
<br />
===Sensor Film Material===<br />
<br />
[[File:Rudppf.gif|right]]<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we foudn the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
<br />
<br />
<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/File:Rudppf.gifFile:Rudppf.gif2011-05-04T02:55:31Z<p>Turbclnt: </p>
<hr />
<div></div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T02:55:00Z<p>Turbclnt: /* Building a dissolved oxygen probe */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
==Plan to overcome technical hurdles==<br />
<br />
===Sensor Film Material===<br />
<br />
The sensor film material must not only fluoresce when exposed to light, but it must also fluoresce at different intensity levels depending on the amount of oxygen in contact with the film. Thankfully, some really smart chemists have already thought of a material to do this...get ready...its a mouthful! The chemical is formally named ''Tris(4,7-diphenyl-1,10-phenanthroline)ruthenium(II)''. Since this is such a mouthful, we'll be referring to this chemical in the rest of the document as Ru(dppf) which is chemistry-speak for the above name.<br />
<br />
Because ruthenium is a metal missing 2 valence electrons (that's the ''II'' in the full name for Ru(dppf)), you can only purchase this chemical in one of many '''complexes'''. A '''complex''' in chemistry is when ions of an opposite charge are associated to an already charged, but unstable molecule. This creates a bond that stabilizes the unstable molecule making it safe and/or easy to handle. Typically, the complexing agent doesn't change the properties of the molecule its bonded to - it just holds on for the ride.<br />
<br />
For our application, choice of a complexing molecule isn't very important, so we foudn the cheapest complex of Ru(dppf) that we could, and ordered some! It happens to be the Ru(dppf) complex (shown to the right).<br />
<br />
===Light Sealing===<br />
<br />
In attempting to build a light tight structure, its important to consider where light could potentially leak into your device. It will help in driving performance requirements for the housing. For the optode, light can enter the structure from 3 main points. Remember, for the optode to work, light in the visible spectrum must be blocked!<br />
<br />
* If the optode film is clear, ambient light from the room in which you are measuring<br />
<br />
<br />
<br />
<br />
<br />
==How to build it==<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T02:36:46Z<p>Turbclnt: /* How an optode works */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be made for cheap?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
<br />
===What you need===<br />
<br />
===How to build it===<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/BioBoard/Documentation/OxygenBioBoard/Documentation/Oxygen2011-05-04T02:36:05Z<p>Turbclnt: /* How an optode works */</p>
<hr />
<div>=Introduction to dissolved oxygen=<br />
<br />
Why is oxygen important? For us humans, if we have oxygen, we survive...yay! If not, we don't...boo. So, superficially, this may not seem like a very important parameter to know - you either have oxygen, or you don't. However, for many microorganisms, there are a lot of shades of gray.<br />
<br />
For a bacteria or a yeast, different amounts of oxygen produce different results. For instance, starving a yeast cell of oxygen produces ethanol as a metabolite product instead of carbon dioxide. Starving a lake of oxygen not only prevents fishies from living in it, but also promotes the formation of large algae surfaces. Cool, right?<br />
<br />
The biggest problem with measuring dissolved oxygen currently is the cost of the equipment available to do it. Typically, dissolved oxygen probes run well into the $400+ range, thus placing them well out of the realm of hobbyists. The cost is not wholly unwarranted - dissolved oxygen meters used a platinum catalyzed reaction with very specific membranes to measure oxygen response. By cutting out the platinum catalyst and the specialized membrane, the cost of a DO meter could drop considerably...enter the optode!<br />
<br />
=Building a dissolved oxygen probe=<br />
<br />
==How an optode works==<br />
In order to reduce cost, we'll be building a dissolved oxygen '''optode''' instead of the more common dissolved oxygen '''electrode'''.<br />
<br />
In an electrode, a small change in a voltage or current is used to detect a change in oxygen concentration. In an optode, a small change in reflected light intensity is used to detect changes in oxygen concentration:<br />
<br />
[[File:DO_Electrodes.jpg|center]]<br />
<br />
There are advantages and disadvantages to each system.<br />
<br />
Properties of commercial dissolved oxygen '''electrodes''':<br />
* Very robust - easily waterproofed<br />
* Very accurate<br />
* Need to recalibrate is rare due to non-reactive nature of the membrane and platinum<br />
* Very small amperages are produced - an amplifier circuit must be built at the amp meter position<br />
* Very, very expensive - $400 and up<br />
<br />
Properties of commercial dissolved oxygen '''optodes''':<br />
* Film must be intact for proper sensing - not as robust<br />
* Film must be permeable to oxygen, but impermeable to media (i.e. water)<br />
* Calibration is difficult - more frequent recalibration necessary due to film degradation<br />
* Chemicals in sensing foil respond at visual wavelengths, so background light can interfere with accuracy and precision<br />
* Very cheap components needed<br />
* No need for an amplifier circuit!<br />
* Commercial probes are very, very expensive - $400 and up as well, but based on the design components, could it be cheaper to make?<br />
<br />
Although the optode has several drawbacks that make it impractical for some uses, there are enough benefits in its simplistic design to make it a potential probe that can handle many situations for $20 or less!<br />
<br />
<br />
===What you need===<br />
<br />
===How to build it===<br />
<br />
===Things to keep in mind===<br />
<br />
=Interfacing and measuring=<br />
<br />
=Calibrating a home-built optode=<br />
<br />
=Making it cooler=<br />
<br />
=Geeking out=<br />
<br />
=Links=</div>Turbclnthttps://noisebridge.net/wiki/File:DO_Electrodes.jpgFile:DO Electrodes.jpg2011-05-04T02:23:07Z<p>Turbclnt: Comparison of dissolved oxygen probe types - traditional electrode seen on the left, optode seen on the right.</p>
<hr />
<div>Comparison of dissolved oxygen probe types - traditional electrode seen on the left, optode seen on the right.</div>Turbclnthttps://noisebridge.net/wiki/BioBoardBioBoard2011-03-27T02:16:58Z<p>Turbclnt: /* Dissolved oxygen (DO) probes */</p>
<hr />
<div>=Abstract=<br />
<br />
&quot;The BioBoard&quot; is an Arduino-controlled sensor package that allowusers to monitor a range of physiochemical factors related to microbiological processes (e.g. algae growing, youghurt production, kombucha fermentation, sourdough culturing, etc.) in liquid media/cultures, with real-time wireless data transmission and graphic data visualization designed to make key correlations between these factors easily graspable.<br />
<br />
[[File:BioBoardOverview.png|200px|thumb|left|BioBoard overview]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
=Goals / Features=<br />
<br />
As a minimum, we want to be able to monitor temperature, pH and dissolved oxygen. We'd also like to be able to measure biomass, either directly or by proxy. The current plan is to build a thermometer, a dissolved oxygen sensor and a biomass probe ourselves, and supplementing with a commercial pH meter. Failing that, we'll buy a thermometer and an oxygen probe as well and attempt to hack them instead, and concentrate on standardising data protocols, building the supporting controller hardware and making the graphics look pretty.<br />
<br />
=Hardware=<br />
<br />
==Sensors== <br />
<br />
Important considerations are affordability, accessibility and required precision. Biologically relevant temperature range is approx. 0-100°C; accuracy should not be less than ±0.5°C at 25-35°C. pH range is (1-14), and required precision is approx. ±0.5, preferably better. dO probe should be able to measure % conc. with an accuracy of approx. ±2%, preferably better. Biomass probe will likely be measuring absorbance as a proxy for total biomass, and can be validated using classic spectrophotometer and CFU count.<br />
<br />
===Thermometer=== <br />
<br />
'''[http://en.wikipedia.org/wiki/Thermocouple Thermocouples (TCs)]'''<br />
<br />
Pros<br />
* Very robust, good for nasty environments <br />
* Wide temperature range (−200°C to +1350°C for type K)<br />
* Relatively cheap (approx. $15 for a DIY model incl. amplifier)<br />
Cons<br />
* Voltage is very small so requires an amplifier with digital out (41 µV/°C for type K)<br />
<br />
'''Digital Temperature Sensors (DTS)'''<br />
<br />
Pros<br />
* Avaliable as one-wire devices, use single digital pin <br />
* Require no amplification or moderation to connect to Arduino<br />
* Good precision in biological range <br />
** ±0.5°C accuracy from –10°C to +85°C for DS1820<br />
* Very cheap ($0.75 to $3.95)<br />
Cons<br />
* Comparatively limited temperature range<br />
** –55°C to +125°C for DS1820<br />
** -40°C to +125°C for TC1047A<br />
* Accuracy only ±2°C for TC1047A at 25°C<br />
* Sensitive to mechanical damage and liquid, so require protection/casing<br />
<br />
'''Thermistors'''<br />
<br />
Pros<br />
* Single analog pin use<br />
* Very cheap ($1.75 from Hacktronics)<br />
Cons<br />
* Comparatively limited temperature range (-40°C to +125°C)<br />
* Accuracy approx. ±1°C at 25°C<br />
<br />
<br />
'''Commercial resources'''<br />
<br />
TCs<br />
* [http://www.omega.com/ppt/pptsc.asp?ref=HTTC36 Hollow Tube Thermocouple Probe] - $19 from Omega <br />
TC wire<br />
* [http://www.mcmaster.com/#type-k-thermocouple-wire/=bkaksl, both wires in a sheath] ~$1/foot, by the foot from McMaster Carr <br />
* Omega [http://www.omega.com/ppt/pptsc.asp?ref=SPIR&amp;Nav=temh02 bare wire is here]. Omega is the ultimate source, but they seem to only sell it by the roll (25 foot minimum, buy both wires separately) or in the form of super nice manufactured probes ($)<br />
Amplifier <br />
* [http://www.sparkfun.com/products/307 TC amplifier] - $12 from Sparkfun<br />
DTS<br />
* [http://www.hacktronics.com/Sensors/Digital-Temperature-Sensor-DS18B20/flypage.tpl.html DS18B20 digital temperature sensor] - $3.95 from Hacktronics<br />
** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-8&amp;file=DSA-149089.pdf Datasheet for DS1820 1-wire DTS]<br />
* [http://us.element-14.com/jsp/displayProduct.jsp?sku=89C8093&amp;CMP=KNC-KEY-SKU-MIC&amp;s_kwcid=TC|20219|tc1047avnbtr||S|b|6383206454 TC1047A microchip] - $0.60 from element14<br />
** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-304&amp;file=55284.pdf Datasheet for TC1047AVNBTR DTS microchip]<br />
Thermistor<br />
* [http://www.hacktronics.com/Sensors/Thermistor-Temperature-Sensor/flypage.tpl.html Thermistor] - $1.75 from Hacktronics<br />
** [http://www.vishay.com/doc?29049 Datasheet for thermistor]<br />
<br />
'''Private resources'''<br />
<br />
* Charlie has access to a good amount of Type K metal sheathed TC wire, plus assorted probes and a TC reader he can donate - as we go along our improving expertise will lead us to resources other people can use... like the relatively cheap McMaster Carr wire.<br />
* We presently have a not-quite-functional prototype digital thermometer which uses a DS18B20 DTS; the sketch is compiling correctly, but there's de-bugging to be done (error msg reads: ''avrdude: stk500_getsync(): not in sync: resp=0x31'').<br />
<br />
[[File:One-wire_prototype.jpg|200px|thumb|left|One-wire prototype]]<br />
<br />
<br />
'''Other resources'''<br />
<br />
* [http://www.instructables.com/id/Making-A-Thermocouple/ Instructable for how to build a thermocouple]. This soldering method will work with the Omega wire, and better junctions can be made with a welder or capacitive discharge.<br />
* [http://www.chinwah-engineering.com/USBThermocoupleProject.html USB Thermocouple Project]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
===pH-meter=== <br />
<br />
'''Commercial resources'''<br />
<br />
Probes<br />
* [http://www.heavydutysupplies.com/servlet/the-15/Checker,-HI-98103,-HI98103/Detail HANNA Instruments HI 98103] $55<br />
* [http://www.amazon.com/Milwaukee-pH600-Portable-pH-meter/dp/B004CZ8632 Milwaukee pH600] $20 - doesn't look like it needs specific buffers for calibration, but the accuracy is probably not great. Maybe it's enough, though.<br />
* [http://www.google.com/products/catalog?hl=en&amp;q=ph+electrode&amp;sqi=2&amp;cid=15011737823946485839&amp;os=sellers# Google shopping results] approx. $40 upwards <br />
* [http://www.pulseinstruments.net/sotaphelectrode.aspx SOTA pH Electrode] $100 - expensive, but so so sweet: designed for continuous measurement, and comes with any kind of connector.<br />
pH tester units <br />
* [http://www.jencostore.com/ph-meter/ph-testers.html?price=1%2C100 Jenco 610 pH tester] for $30 - perhaps it could be hacked?<br />
<br />
'''Schematic'''<br />
<br />
* [http://www.ph-meter.info/pH-meter-construction pH meter construction] - this could perhaps be adapted to use an Arduino instead of a voltmeter - not necessarily cheaper than buying, although it’d certainly be both fun and informative. <br />
* We could also build [http://xkcd.com/730/ this]<br />
<br />
<br />
===Dissolved oxygen (DO) probes===<br />
<br />
'''Membrane electrode''' (a.k.a. strip an automotive O2 sensor for parts to make a membrane electrode)<br />
<br />
Pros<br />
* New sensors for out of date cars are available on eBay for $10<br />
* Contain required platinum, anodes, and teflon membrane <br />
Cons<br />
* Sensors typically operate at ~300C<br />
Progress <br />
* Ordered 3 $6-$10 probes on ebay to futz with<br />
* Plan is to knock out the zirconium matrix and add a KCl electrolyte to see if we can get a reaction started at room temperature.<br />
<br />
'''Optode''' (a.k.a. build an intensity- or time-based optode from scratch)<br />
<br />
Recently, people have been using a [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=85793|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPEC ruthenium complex] as a visual (fluorescent) indicator of oxygen concentration. This complex is excited by a blue LED, then its transmission is measured by a filtered photoresistor (more details [http://www.env.gov.nl.ca/env/waterres/rti/rtwq/07_14.pdf here in pdf])<br />
<br />
Pros<br />
* All solid state (super low maintenance) <br />
* No calibration needed <br />
Cons<br />
* Could be some serious tecnical hurdles to overcome on this one<br />
* Ru molecule is expensive (~$70/mg)<br />
<br />
Film Contruction Ideas<br />
* Disperse catalyst in PVC powder, bake in oven on top of PET film under compression. May hit a rheology problem with the PET film. Melting point of PET is close to that of PVC.<br />
* Film coat: PVC dissolves in 2-butanone, whereas PET will not. Make a thin liquid layer, then allow to evaporate. PVC morphology may not provide necessary mechanical stiffness after this process.<br />
<br />
'''Commercial resources'''<br />
<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=85793|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPEC ruthenium complex]<br />
* [http://www.vernier.com/probes/do-bta.html DO-BTA Dissolved Oxygen Sensor] $209<br />
* [http://www.google.com/products/catalog?q=dissolved+oxygen+sensor&amp;hl=en&amp;safe=off&amp;cid=1714170039035567861&amp;os=sellers# Yellow Springs Dissolved Oxygen Meters] $80-104<br />
<br />
===Biomass===<br />
<br />
'''[http://en.wikipedia.org/wiki/Nir_spectroscopy NIR spectroscopy] / [http://en.wikipedia.org/wiki/Absorbance Absorbance]'''<br />
<br />
Pros<br />
* Currently lots of DIY spectroscopy projects under development<br />
* Relatively easy build, can be made using a LED and an old cell phone [http://en.wikipedia.org/wiki/Charged_coupled_device CCD]<br />
* Can be used for chemical analysis as well<br />
* Verification of results with known absorbance values should be easy <br />
Cons<br />
* Will likely need re-calibration for every use<br />
* Could be very hard to pack into a probe<br />
<br />
<br />
'''Calibrated capacitance + conductivity sensor'''<br />
<br />
Industry has commercial probes available which measure living biomass; we think we may be able to retroengineer such a thing. With enough calibration, it might be possible to do this by measuring [http://www.aber-instruments.co.uk/brewing/controlling-cell-culture-processes capacitance alone].<br />
<br />
[The basic principle behind these probes is the different electrical properties of living and dead cells; both are conductive - being essential very long and folded chains of carbon molecules - but living cells also act as capacitors (batteries); active transport across the cell membrane of electrically charged ions/molecules establishes a negative potential/charge on the order of -70mV in resting mammalian neurons.]<br />
<br />
'''Commercial resources'''<br />
<br />
* [http://www.optek.com/Product_Detail.asp?ProductID=12 ASD19-N Single Channel NIR Absorption Probe]<br />
** [http://www.optek.com/Schematic_Single_Channel_NIR_LED_Probe.asp NIR probe schematic]<br />
** [http://www.optek.com/pdf/optek-ASD19-N_Data-Sheet_english.pdf ASD19-N datasheet] <br />
<br />
'''Other resources'''<br />
<br />
* [http://www.finesse.com/files/pdfs/app-tech-notes/TruCell.TN.AUvsOD.pdf .pdf] with technical notes about a commercial OD probe<br />
* [http://www.optek.com/Application_Note/Biotechnology/English/2/Fermentation_and_Cell_Growth_Monitoring.asp Industrial application of NIR spectroscopy] in fermentation and cell growth monitoring <br />
* [http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/index.html Cell phone spectrophotometer]<br />
* [http://www.rsc.org/Education/EiC/issues/2007Sept/BuildYourOwnSpectrophotometer.asp Article] on how to build your own spectrophtometer<br />
* [http://topologicoceans.wordpress.com/2011/03/15/diy-spectro-ii/ DIY Spectrometer]<br />
** [http://topologicoceans.wordpress.com/2011/01/29/diy-spectro-faq/ DIY Spectrometer FAQ] - lots of useful links to other DIY spectro projects<br />
<br />
==Microcontroller assembly==<br />
<br />
Arduino is the microcontroller of choice; which board will depend on which assembly we choose.<br />
<br />
'''Ethernet shield set-up'''<br />
<br />
Pros<br />
* Cheap and simple <br />
Cons<br />
* Perhaps not enough power + pins for sensors <br />
<br />
'''Sensor shield + biffer board set-up'''<br />
<br />
Pros<br />
* More power + pins for sensors<br />
* [http://bifferos.bizhat.com/ The biffer board] is excellent and tiny (1W)<br />
Cons<br />
* No experience with use of the sensor shield<br />
* More parts = more $<br />
* More parts also = more work + more potential complications<br />
<br />
<br />
=Software=<br />
<br />
==Data logging and visualization==<br />
<br />
'''Data transmission'''<br />
<br />
Data should be timestamped, categorized (pH, temperature, etc) and transmitted in real-time<br />
* JSON data serialization format<br />
* HTTP for transmission to server<br />
** Include &quot;export to CSV&quot; function with option for data set selection - should allow people to use a variety of programming languages and data analysis tools without a lot of work on their part or ours <br />
<br />
'''Web server''' <br />
<br />
Custom Rails app <br />
* Receives data<br />
* Logs to database <br />
* Generates graphs on demand<br />
** Add Comet server for live-updated graphs <br />
* Include 'export to CSV' function to allow users to extract data for analysis with tool(s) <br />
* All code on github so others can fork and add features<br />
<br />
* We could add features that lets new users sign up and get a unique key which they use when transmitting their own data to the JSON web service on our server. The server then uses the key to associate the data with the user, and the user can look at their graphs and share them with others. <br />
<br />
'''Resources'''<br />
<br />
* Eric Allens has been kind enough to open source the [http://github.com/epall/templogger online templogger] he uses to [http://svallens.com/templogger/ live-monitor his house].<br />
:He adds: ''&quot;The installation is totally undocumented at this point, so I suggest using this as a guideline to build something new, as opposed to using it verbatim. I do recommend considering starting from scratch with [http://oss.oetiker.ch/rrdtool/ RRDtool].&quot;''<br />
* Labitat has a [http://space.labitat.dk/ live power usage graph] made with Comet<br />
* [http://welserver.com/ Web Energy Logger]</div>Turbclnthttps://noisebridge.net/wiki/BioBoardBioBoard2011-03-27T02:16:28Z<p>Turbclnt: /* Dissolved oxygen (DO) probes */</p>
<hr />
<div>=Abstract=<br />
<br />
&quot;The BioBoard&quot; is an Arduino-controlled sensor package that allowusers to monitor a range of physiochemical factors related to microbiological processes (e.g. algae growing, youghurt production, kombucha fermentation, sourdough culturing, etc.) in liquid media/cultures, with real-time wireless data transmission and graphic data visualization designed to make key correlations between these factors easily graspable.<br />
<br />
[[File:BioBoardOverview.png|200px|thumb|left|BioBoard overview]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
=Goals / Features=<br />
<br />
As a minimum, we want to be able to monitor temperature, pH and dissolved oxygen. We'd also like to be able to measure biomass, either directly or by proxy. The current plan is to build a thermometer, a dissolved oxygen sensor and a biomass probe ourselves, and supplementing with a commercial pH meter. Failing that, we'll buy a thermometer and an oxygen probe as well and attempt to hack them instead, and concentrate on standardising data protocols, building the supporting controller hardware and making the graphics look pretty.<br />
<br />
=Hardware=<br />
<br />
==Sensors== <br />
<br />
Important considerations are affordability, accessibility and required precision. Biologically relevant temperature range is approx. 0-100°C; accuracy should not be less than ±0.5°C at 25-35°C. pH range is (1-14), and required precision is approx. ±0.5, preferably better. dO probe should be able to measure % conc. with an accuracy of approx. ±2%, preferably better. Biomass probe will likely be measuring absorbance as a proxy for total biomass, and can be validated using classic spectrophotometer and CFU count.<br />
<br />
===Thermometer=== <br />
<br />
'''[http://en.wikipedia.org/wiki/Thermocouple Thermocouples (TCs)]'''<br />
<br />
Pros<br />
* Very robust, good for nasty environments <br />
* Wide temperature range (−200°C to +1350°C for type K)<br />
* Relatively cheap (approx. $15 for a DIY model incl. amplifier)<br />
Cons<br />
* Voltage is very small so requires an amplifier with digital out (41 µV/°C for type K)<br />
<br />
'''Digital Temperature Sensors (DTS)'''<br />
<br />
Pros<br />
* Avaliable as one-wire devices, use single digital pin <br />
* Require no amplification or moderation to connect to Arduino<br />
* Good precision in biological range <br />
** ±0.5°C accuracy from –10°C to +85°C for DS1820<br />
* Very cheap ($0.75 to $3.95)<br />
Cons<br />
* Comparatively limited temperature range<br />
** –55°C to +125°C for DS1820<br />
** -40°C to +125°C for TC1047A<br />
* Accuracy only ±2°C for TC1047A at 25°C<br />
* Sensitive to mechanical damage and liquid, so require protection/casing<br />
<br />
'''Thermistors'''<br />
<br />
Pros<br />
* Single analog pin use<br />
* Very cheap ($1.75 from Hacktronics)<br />
Cons<br />
* Comparatively limited temperature range (-40°C to +125°C)<br />
* Accuracy approx. ±1°C at 25°C<br />
<br />
<br />
'''Commercial resources'''<br />
<br />
TCs<br />
* [http://www.omega.com/ppt/pptsc.asp?ref=HTTC36 Hollow Tube Thermocouple Probe] - $19 from Omega <br />
TC wire<br />
* [http://www.mcmaster.com/#type-k-thermocouple-wire/=bkaksl, both wires in a sheath] ~$1/foot, by the foot from McMaster Carr <br />
* Omega [http://www.omega.com/ppt/pptsc.asp?ref=SPIR&amp;Nav=temh02 bare wire is here]. Omega is the ultimate source, but they seem to only sell it by the roll (25 foot minimum, buy both wires separately) or in the form of super nice manufactured probes ($)<br />
Amplifier <br />
* [http://www.sparkfun.com/products/307 TC amplifier] - $12 from Sparkfun<br />
DTS<br />
* [http://www.hacktronics.com/Sensors/Digital-Temperature-Sensor-DS18B20/flypage.tpl.html DS18B20 digital temperature sensor] - $3.95 from Hacktronics<br />
** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-8&amp;file=DSA-149089.pdf Datasheet for DS1820 1-wire DTS]<br />
* [http://us.element-14.com/jsp/displayProduct.jsp?sku=89C8093&amp;CMP=KNC-KEY-SKU-MIC&amp;s_kwcid=TC|20219|tc1047avnbtr||S|b|6383206454 TC1047A microchip] - $0.60 from element14<br />
** [http://www.datasheetarchive.com/pdf/getfile.php?dir=Datasheets-304&amp;file=55284.pdf Datasheet for TC1047AVNBTR DTS microchip]<br />
Thermistor<br />
* [http://www.hacktronics.com/Sensors/Thermistor-Temperature-Sensor/flypage.tpl.html Thermistor] - $1.75 from Hacktronics<br />
** [http://www.vishay.com/doc?29049 Datasheet for thermistor]<br />
<br />
'''Private resources'''<br />
<br />
* Charlie has access to a good amount of Type K metal sheathed TC wire, plus assorted probes and a TC reader he can donate - as we go along our improving expertise will lead us to resources other people can use... like the relatively cheap McMaster Carr wire.<br />
* We presently have a not-quite-functional prototype digital thermometer which uses a DS18B20 DTS; the sketch is compiling correctly, but there's de-bugging to be done (error msg reads: ''avrdude: stk500_getsync(): not in sync: resp=0x31'').<br />
<br />
[[File:One-wire_prototype.jpg|200px|thumb|left|One-wire prototype]]<br />
<br />
<br />
'''Other resources'''<br />
<br />
* [http://www.instructables.com/id/Making-A-Thermocouple/ Instructable for how to build a thermocouple]. This soldering method will work with the Omega wire, and better junctions can be made with a welder or capacitive discharge.<br />
* [http://www.chinwah-engineering.com/USBThermocoupleProject.html USB Thermocouple Project]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
===pH-meter=== <br />
<br />
'''Commercial resources'''<br />
<br />
Probes<br />
* [http://www.heavydutysupplies.com/servlet/the-15/Checker,-HI-98103,-HI98103/Detail HANNA Instruments HI 98103] $55<br />
* [http://www.amazon.com/Milwaukee-pH600-Portable-pH-meter/dp/B004CZ8632 Milwaukee pH600] $20 - doesn't look like it needs specific buffers for calibration, but the accuracy is probably not great. Maybe it's enough, though.<br />
* [http://www.google.com/products/catalog?hl=en&amp;q=ph+electrode&amp;sqi=2&amp;cid=15011737823946485839&amp;os=sellers# Google shopping results] approx. $40 upwards <br />
* [http://www.pulseinstruments.net/sotaphelectrode.aspx SOTA pH Electrode] $100 - expensive, but so so sweet: designed for continuous measurement, and comes with any kind of connector.<br />
pH tester units <br />
* [http://www.jencostore.com/ph-meter/ph-testers.html?price=1%2C100 Jenco 610 pH tester] for $30 - perhaps it could be hacked?<br />
<br />
'''Schematic'''<br />
<br />
* [http://www.ph-meter.info/pH-meter-construction pH meter construction] - this could perhaps be adapted to use an Arduino instead of a voltmeter - not necessarily cheaper than buying, although it’d certainly be both fun and informative. <br />
* We could also build [http://xkcd.com/730/ this]<br />
<br />
<br />
===Dissolved oxygen (DO) probes===<br />
<br />
'''Membrane electrode''' (a.k.a. strip an automotive O2 sensor for parts to make a membrane electrode)<br />
<br />
Pros<br />
* New sensors for out of date cars are available on eBay for $10<br />
* Contain required platinum, anodes, and teflon membrane <br />
Cons<br />
* Sensors typically operate at ~300C<br />
Progress <br />
* Ordered 3 $6-$10 probes on ebay to futz with<br />
* Plan is to knock out the zirconium matrix and add a KCl electrolyte to see if we can get a reaction started at room temperature.<br />
<br />
'''Optode''' (a.k.a. build an intensity- or time-based optode from scratch)<br />
<br />
Recently, people have been using a [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=85793|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPEC ruthenium complex] as a visual (fluorescent) indicator of oxygen concentration. This complex is excited by a blue LED, then its transmission is measured by a filtered photoresistor (more details [http://www.env.gov.nl.ca/env/waterres/rti/rtwq/07_14.pdf here in pdf])<br />
<br />
Pros<br />
* All solid state (super low maintenance) <br />
* No calibration needed <br />
Cons<br />
* Could be some serious tecnical hurdles to overcome on this one<br />
* Ru molecule is expensive (~$70/mg)<br />
<br />
Film Contruction Ideas<br />
* Disperse catalyst in PVC powder, bake in oven on top of PET film under compression. May hit a rheology problem with the PET film. Melting point of PET is close to that of PVC.<br />
* Film coat: PVC dissolves in 2-butanone, wheras PET will not. Make a thin liquid layer, then allow to evaporate. PVC morphology may not provide necessary mechanical stiffness after this process.<br />
<br />
'''Commercial resources'''<br />
<br />
* [http://www.sigmaaldrich.com/catalog/ProductDetail.do?lang=en&amp;N4=85793|FLUKA&amp;N5=SEARCH_CONCAT_PNO|BRAND_KEY&amp;F=SPEC ruthenium complex]<br />
* [http://www.vernier.com/probes/do-bta.html DO-BTA Dissolved Oxygen Sensor] $209<br />
* [http://www.google.com/products/catalog?q=dissolved+oxygen+sensor&amp;hl=en&amp;safe=off&amp;cid=1714170039035567861&amp;os=sellers# Yellow Springs Dissolved Oxygen Meters] $80-104<br />
<br />
===Biomass===<br />
<br />
'''[http://en.wikipedia.org/wiki/Nir_spectroscopy NIR spectroscopy] / [http://en.wikipedia.org/wiki/Absorbance Absorbance]'''<br />
<br />
Pros<br />
* Currently lots of DIY spectroscopy projects under development<br />
* Relatively easy build, can be made using a LED and an old cell phone [http://en.wikipedia.org/wiki/Charged_coupled_device CCD]<br />
* Can be used for chemical analysis as well<br />
* Verification of results with known absorbance values should be easy <br />
Cons<br />
* Will likely need re-calibration for every use<br />
* Could be very hard to pack into a probe<br />
<br />
<br />
'''Calibrated capacitance + conductivity sensor'''<br />
<br />
Industry has commercial probes available which measure living biomass; we think we may be able to retroengineer such a thing. With enough calibration, it might be possible to do this by measuring [http://www.aber-instruments.co.uk/brewing/controlling-cell-culture-processes capacitance alone].<br />
<br />
[The basic principle behind these probes is the different electrical properties of living and dead cells; both are conductive - being essential very long and folded chains of carbon molecules - but living cells also act as capacitors (batteries); active transport across the cell membrane of electrically charged ions/molecules establishes a negative potential/charge on the order of -70mV in resting mammalian neurons.]<br />
<br />
'''Commercial resources'''<br />
<br />
* [http://www.optek.com/Product_Detail.asp?ProductID=12 ASD19-N Single Channel NIR Absorption Probe]<br />
** [http://www.optek.com/Schematic_Single_Channel_NIR_LED_Probe.asp NIR probe schematic]<br />
** [http://www.optek.com/pdf/optek-ASD19-N_Data-Sheet_english.pdf ASD19-N datasheet] <br />
<br />
'''Other resources'''<br />
<br />
* [http://www.finesse.com/files/pdfs/app-tech-notes/TruCell.TN.AUvsOD.pdf .pdf] with technical notes about a commercial OD probe<br />
* [http://www.optek.com/Application_Note/Biotechnology/English/2/Fermentation_and_Cell_Growth_Monitoring.asp Industrial application of NIR spectroscopy] in fermentation and cell growth monitoring <br />
* [http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/index.html Cell phone spectrophotometer]<br />
* [http://www.rsc.org/Education/EiC/issues/2007Sept/BuildYourOwnSpectrophotometer.asp Article] on how to build your own spectrophtometer<br />
* [http://topologicoceans.wordpress.com/2011/03/15/diy-spectro-ii/ DIY Spectrometer]<br />
** [http://topologicoceans.wordpress.com/2011/01/29/diy-spectro-faq/ DIY Spectrometer FAQ] - lots of useful links to other DIY spectro projects<br />
<br />
==Microcontroller assembly==<br />
<br />
Arduino is the microcontroller of choice; which board will depend on which assembly we choose.<br />
<br />
'''Ethernet shield set-up'''<br />
<br />
Pros<br />
* Cheap and simple <br />
Cons<br />
* Perhaps not enough power + pins for sensors <br />
<br />
'''Sensor shield + biffer board set-up'''<br />
<br />
Pros<br />
* More power + pins for sensors<br />
* [http://bifferos.bizhat.com/ The biffer board] is excellent and tiny (1W)<br />
Cons<br />
* No experience with use of the sensor shield<br />
* More parts = more $<br />
* More parts also = more work + more potential complications<br />
<br />
<br />
=Software=<br />
<br />
==Data logging and visualization==<br />
<br />
'''Data transmission'''<br />
<br />
Data should be timestamped, categorized (pH, temperature, etc) and transmitted in real-time<br />
* JSON data serialization format<br />
* HTTP for transmission to server<br />
** Include &quot;export to CSV&quot; function with option for data set selection - should allow people to use a variety of programming languages and data analysis tools without a lot of work on their part or ours <br />
<br />
'''Web server''' <br />
<br />
Custom Rails app <br />
* Receives data<br />
* Logs to database <br />
* Generates graphs on demand<br />
** Add Comet server for live-updated graphs <br />
* Include 'export to CSV' function to allow users to extract data for analysis with tool(s) <br />
* All code on github so others can fork and add features<br />
<br />
* We could add features that lets new users sign up and get a unique key which they use when transmitting their own data to the JSON web service on our server. The server then uses the key to associate the data with the user, and the user can look at their graphs and share them with others. <br />
<br />
'''Resources'''<br />
<br />
* Eric Allens has been kind enough to open source the [http://github.com/epall/templogger online templogger] he uses to [http://svallens.com/templogger/ live-monitor his house].<br />
:He adds: ''&quot;The installation is totally undocumented at this point, so I suggest using this as a guideline to build something new, as opposed to using it verbatim. I do recommend considering starting from scratch with [http://oss.oetiker.ch/rrdtool/ RRDtool].&quot;''<br />
* Labitat has a [http://space.labitat.dk/ live power usage graph] made with Comet<br />
* [http://welserver.com/ Web Energy Logger]</div>Turbclnthttps://noisebridge.net/wiki/Fermentation_logsFermentation logs2011-03-09T09:01:00Z<p>Turbclnt: /* Fermenting Log */</p>
<hr />
<div>= March 9th, 2011: (yet unnamed) v0.1 =<br />
<br />
== Ingredients and Batch Size ==<br />
* Yeast type &amp; origin: '''[[Fermenting Yeasts#Gert Strand, Black Label|Gert Strand, Black Label]]''' (Malmo, Sweden)<br />
* Theoretical %ABV: 14-17%<br />
* Sugar Source: TBD<br />
* Target Size: ~25L<br />
<br />
== Fermenting Log ==<br />
<br />
Starts @ 20:00, March 9th!<br />
<br />
= March 2nd, 2011: DAVROS v0.1 =<br />
<br />
== Ingredients and Batch Size ==<br />
* Yeast type &amp; origin: '''[[Fermenting Yeasts#Gert Strand, Black Label|Gert Strand, Black Label]]''' (Malmo, Sweden)<br />
* Theoretical %ABV: 14-17%<br />
* Sugar Source: C&amp;H Cane Sugar<br />
* Target Size: ~25L<br />
<br />
== Fermenting Log ==<br />
*'''03/02/2011 20:05''': C&amp;H Cane Sugar has been dissolved and diluted to 2x 12.5L. Temps: 24.5C, 25.5C. Confirmed ready to pitch yeast.<br />
*'''03/02/2011 20:50''': Yeast was pitched and shaken to dissolve into a cloudy solution. Specific gravity of each tank = 1.090 (exactly equal to yeast maker's recommendation).<br />
*'''03/03/2011 23:59''': Davros tank 1&amp;2: 72 degrees [[User:Miloh|Miloh]]<br />
*'''03/04/2011 13:13''': Davros tank 1&amp;2: 72 degrees<br />
*'''03/08/2011 20:35''': Davros tank 1: 67C, specific gravity = 984.5 (target range = 984 - 987). Its done! [[User:turbclnt|Sean C]]<br />
*'''03/08/2011 20:35''': Davros tank 2: 67C. specific gravity = 984.0 (target range = 984 - 987). Its done too! [[User:turbclnt|Sean C]]</div>Turbclnthttps://noisebridge.net/wiki/Fermentation_logsFermentation logs2011-03-09T09:00:37Z<p>Turbclnt: /* March 9th, 2011: (yet unnamed) v0.1 */</p>
<hr />
<div>= March 9th, 2011: (yet unnamed) v0.1 =<br />
<br />
== Ingredients and Batch Size ==<br />
* Yeast type &amp; origin: '''[[Fermenting Yeasts#Gert Strand, Black Label|Gert Strand, Black Label]]''' (Malmo, Sweden)<br />
* Theoretical %ABV: 14-17%<br />
* Sugar Source: TBD<br />
* Target Size: ~25L<br />
<br />
== Fermenting Log ==<br />
<br />
= March 2nd, 2011: DAVROS v0.1 =<br />
<br />
== Ingredients and Batch Size ==<br />
* Yeast type &amp; origin: '''[[Fermenting Yeasts#Gert Strand, Black Label|Gert Strand, Black Label]]''' (Malmo, Sweden)<br />
* Theoretical %ABV: 14-17%<br />
* Sugar Source: C&amp;H Cane Sugar<br />
* Target Size: ~25L<br />
<br />
== Fermenting Log ==<br />
*'''03/02/2011 20:05''': C&amp;H Cane Sugar has been dissolved and diluted to 2x 12.5L. Temps: 24.5C, 25.5C. Confirmed ready to pitch yeast.<br />
*'''03/02/2011 20:50''': Yeast was pitched and shaken to dissolve into a cloudy solution. Specific gravity of each tank = 1.090 (exactly equal to yeast maker's recommendation).<br />
*'''03/03/2011 23:59''': Davros tank 1&amp;2: 72 degrees [[User:Miloh|Miloh]]<br />
*'''03/04/2011 13:13''': Davros tank 1&amp;2: 72 degrees<br />
*'''03/08/2011 20:35''': Davros tank 1: 67C, specific gravity = 984.5 (target range = 984 - 987). Its done! [[User:turbclnt|Sean C]]<br />
*'''03/08/2011 20:35''': Davros tank 2: 67C. specific gravity = 984.0 (target range = 984 - 987). Its done too! [[User:turbclnt|Sean C]]</div>Turbclnthttps://noisebridge.net/wiki/Category:EventsCategory:Events2011-03-09T08:58:43Z<p>Turbclnt: /* Upcoming Events edit */</p>
<hr />
<div>&lt;!-- Note that this page uses transclusion. Content between the &quot;onlyinclude&quot; tags below will be pushed to the main page --&gt;<br />
Official, Semi-Official, one-off and other events at the Noisebridge space.<br />
<br />
=Event Calendar=<br />
Not all events make it onto this calendar. Many events only make it to the Discussion or Announcements [[Mailinglist | mailing lists]], [[IRC]] or in person at [[:Category:Meeting_Notes | Tuesday meetings]]. Best of all, Noisebridge is about people getting together at the space in San Francisco to do stuff... like in person. Some events just happen. Pay attention!<br />
<br />
If you'd like to host an event yourself, we have advice on [[Hosting_an_Event | hosting an event]] at Noisebridge.<br />
<br />
Event posters are encouraged to crosspost to the Google Calendar. View the [http://www.google.com/calendar/embed?src=vo3i3c0qtjnkjr2ojasd0ftt8s%40group.calendar.google.com&amp;ctz=America/Los_Angeles Google Calendar], view the [http://www.google.com/calendar/feeds/vo3i3c0qtjnkjr2ojasd0ftt8s%40group.calendar.google.com/public/basic Google Calendar in XML], or the [http://www.google.com/calendar/ical/vo3i3c0qtjnkjr2ojasd0ftt8s%40group.calendar.google.com/public/basic.ics Google Calendar in ical] format.<br />
<br />
To post Google Calendar entries for your event, contact a Noisebridge member for access.<br />
<br />
(Wouldn't it be great if there were a gCal mediawiki plugin so crossposting wasn't needed? Do you know of a good one? Help us!) &lt;- working on this, need to upgrade Mediawiki in order to use some plugins.<br />
&lt;!-- Items inside this &quot;onlyinclude&quot; tag will be pushed to the main page --&gt;&lt;onlyinclude&gt;<br />
=== Upcoming Events &lt;small&gt;[https://www.noisebridge.net/index.php?title=Category:Events&amp;action=edit&amp;section=2 edit]&lt;/small&gt; ===<br />
* '''March 3rd, Thursday, 19:00 - [[Adobe Lightroom|Adobe Lightroom Class]]''' - Main area/projector - Learn how to use Adobe Lightroom, from importing your photos, developing, to publishing<br />
* '''March 3rd, Thursday, 19:30 - Development discussion: Android Development Versus Apple Development''' - similarities, differences, working with the hardware &amp; software on each - Hosted by @dam<br />
* '''March 4th, Friday, 19:00 - 07:00 - Mushroom microscopy workshop<br />
* '''March 5th &amp; 6th, 10:00 - [http://www.systemateka.com/PyPyMiniSprint.html PyPy Mini-Sprint]''' - Church classroom<br />
* '''March 9th, 20:00''' - Ferment and filter a mash! [[fermentation logs]]<br />
* '''March 10, Thursday, 19:00 - Group Grammar Clinic''' - Church Classroom - By Donation - A clinic for grammar and writing evaluation. Please bring your web/social or technical writing for us to evaluate. Bring your laptop as well. Collaboration groupware possibly provided. (Please suggest groupware software to use if you wish). Constructive feedback from other group members is encouraged so that this clinic is a group process. - Facilitator: [[User:Owen|Owen]] (opietro@yahoo.com)<br />
<br />
=== Recurring Events &lt;small&gt;[https://www.noisebridge.net/index.php?title=Category:Events&amp;action=edit&amp;section=3 edit]&lt;/small&gt; ===<br />
&lt;!-- Large turnout events should be written in '''bold'''. --&gt;<br />
* '''Monday'''<br />
** [[House_Keeping#Trash_and_Recycling|Trash Night]] - Take out the trash and compost for Tuesday morning!<br />
** 17:00-19:00 [[Taste Bridge and Free School Cooking Class]] - First Trial Run this Monday the 21st- theme is Mediterranean Cooking. Featuring an integrated Basic Lesson in Arabic with Jack. http://www.sffreeschool.com/ <br />
** 18:00 [[iPhone OS developer weekly meetup]] - We make teh applukashuns, joyn us 2 make dem 2! http://meetup.com/iphonedevsf<br />
** 18:30 [[PyClass]] - Learn how to program using the Python programming language.<br />
** '''19:00 [[Circuit Hacking Mondays]]''' - Learn to solder! Mitch will bring kits to make cool, hackable things that you can bring home after you make them. Bring your own projects to hack! There's now an Audio Hacking Adjunct group that meets along with the Circuit Hackers. <br />
** 19:00 1st and 3rd Mondays the BACE Timebank group meets to help organize community mutual aid by trading in equal time credits, wherever there is space. For more info. mira (at) sfbace.org or to join go to timebank.sfbace.org<br />
** 21:00-22:00 [[Free School Chi Gong with Russel in the Church]] - Chi Gong is an ancient form of mind mind-body energy work similar to Tai Chi- think Standing Asian Yoga <br />
** 22:00-24:00 [[Free School Utopian Films Club]] - Each Monday at 10 we'll be hosting the screening of a different Utopian film, followed by a discussion. Our first trial meeting the 21st we'll be showing the new Zeitgeist film http://www.zeitgeistmovingforward.com/<br />
<br />
* '''Tuesday'''<br />
** 12:30 [[Django Study Group]] - install and use the Django Python-based web framework, Turing classroom <br />
** 15:00 [[Linux System Administration Study Group]] - Study Linux admining in the Turing classroom.<br />
** 18:00 [[Tastebridge]] Cooking Class. Come and lets share together what we know about preparing delicious dishes. <br />
** 18:30 Bay Area Community Exchange Project Roundtable Meeting (third Tues. of every month)-discussion of alternative currencies in the back classroom.<br />
** 19:00 [[ruby_class|Ruby Class]] 7pm-9pm<br />
&lt;!--On haitus? Pls update ** 19:00 [[Origami|Learn You A Origami!]] - Learn how make folded-paper models. Beginners welcome!--&gt;<br />
** 19:30 [[Probability]] study group<br />
** 19.30 [[Show and Tell]] -- Show your latest and greatest projects and hacks (working or in-progress), just before the weekly meeting. We meet in the Electronics Lab/Main Space.<br />
** '''20:00 [[#Meetings|Noisebridge Weekly Meeting]]''' - Introducing new people and events to the space, general discussion, and decision making.<br />
* '''Wednesday'''<br />
** 18:00 [[LinuxDiscussion|Linux Discussion]] - Play with Linux in the Turing classroom.<br />
&lt;!--Weekly? Pls update ** 17:00 [[BarCamp Staff Meeting]] - Meeting for BarCamp Staff to discuss plans for San Francisco BarCamp.--&gt;<br />
** 18:00 [[Tastebridge]] Our brewing classes are happening for more than 8 months already and knowledge and master craft is accumulating ...<br />
** 19:00 [[SCoW]] - Sewing, Crafting, Or Whatever! Come make cool stuff with geeks.<br />
** 19:30 [[Machine Learning]] - Teach computers to learn stuff using artificial intelligence and other techniques.<br />
* '''Thursday'''<br />
** [[House_Keeping#Trash_and_Recycling|Trash Night]] - Take out the trash for Friday morning!<br />
** 19:30 [[Games]] - Play games with geeks.<br />
** '''20:00 [[Five_Minutes_of_Fame | Five Minutes of Fame]]''' (3rd Thursdays)<br />
* '''Friday''' <br />
** 12:30 [[Django Study Group]] - install and use the Django Python-based web framework, Turing classroom <br />
** 15:00 [[Linux System Administration Study Group]] - Study Linux admining in the Turing classroom. <br />
** 19:00 [[Science, Engineering &amp; Design Huddle]] - Weekly group to discuss design approach, share techniques, and solve any problem you may be having with your project(s).<br />
* '''Saturday'''<br />
** 16:00 [[Pwn Your Own]] - Pwn Your Own is your chance to learn about every day security threats to every day internet activities. Designed for hackers at all levels, (1st Saturday).<br />
* '''Sunday'''<br />
** 14:00 [http://baha.bitrot.info/ Bay Area Hacker's Association - security meeting] (2nd Sundays)<br />
** 15:00 [[Go]] - Playing of the Go boardgame. On nice days we often take the boards to Dolores Park and play there.<br />
** 15:00 [[Locks!]] - Lock sport, sundays when there is demand. ( See [[locks!]] for more information. )<br />
&lt;!--Happening? pls update ** 17:00 [[Rsync Users Group]] - A twelve step program for those who have poor *nix habits.--&gt;<br />
** 18:00 [[Spacebridge]] - Noisebridge's space program<br />
** 18:00 [[Code Bridge]] - Codebridge projects get help writing code or help others with their code<br />
<br />
&lt;/onlyinclude&gt;<br />
<br />
=== Proposed Future Events and Classes ===<br />
<br />
:'''(TBD)''': [[Probability]] - Weekly probability study group based on [http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-041-probabilistic-systems-analysis-and-applied-probability-spring-2006/related-resources/ Fundamentals of Applied Probability Theory] by Al Drake<br />
:'''(TBD)''': [[German]] - Learn German, all levels. 7pm beginners, 8pm advanced. RSVP 24 hours in advance for the benefit of the instructor. Events ran May-November 2009 on Mondays. Currently on hiatus. Get on the mailing list.<br />
:'''(TBD)''': [[Mandarin Corner|Mandarin]] - Learn or practice Mandarin, all levels. Also currently on hiatus. Get on the mailing list.<br />
:'''(TBD)''': [[Movie Night!]] - [[User:ThOMG|Thom]] wants to build community through nerdy sci-fi! (+Bill+Ted+Excellence++)<br />
:'''(TBD)''': [[Introduction to the AVR Microcontroller]] - [[User:Mightyohm|Jeff]] and [[User:Maltman23|Mitch]] are planning an introductory class for people wanting to make cool projects with AVRs.<br />
:'''(TBD)''': [[Basic Chemistry Lab Techniques]]<br />
:'''(TBD)''': [[Cuddle Puddle for the Economy]] - Stress-hacking with informal massage exchange.<br />
:'''(TBD)''': [[Milk and Cookies]] - Come read your favorite selections out loud. With Milk and Cookies (and yeah, probably beer too).<br />
:'''(TBD)''': [[Processing Workshop 2]] - [[User:Scmurray|Scott]] is interested in teaching this, and is busy thinking about what, where, when, why, and how.<br />
:'''(TBD)''': [[Hack your Hardware]] -- We call BS on &quot;no user-serviceable parts inside&quot;<br />
:'''(TBD)''': [[Homebrew Instruction Class]] - The Wort (pt 1/3)<br />
:'''(TBD)''': [[Trip to Shooting Range]] - Field trip to a shooting range, to shoot guns. Express interest at [[Trip to Shooting Range]]<br />
:'''(TBD)''': [[Surface Mount Soldering Workshop]] - Learn how to solder cicuits with small surface mount parts. [[User:maltman23|Mitch Altman]] and Martin Bogomolni and others will show their tricks. [[User:maltman23|Mitch]] will bring hackable kits that uses surface mounts for you to solder.<br />
:'''(TBD)''' - [[Locksport and Lockpicking]]<br />
:'''(TBD)''' - [[Version control tutorial]]<br />
:'''(TBD)''' - [[Foreign language learning for rocket scientists]] - I'm near-native (fool people when I try) in (French and) Japanese, and a pro trans/terpreter and will share my shortcuts (skill-order, vocab, speed/articulation, translation≅grammar). No expertise on tonal languages yet... so if you know how to remember tones or how tone-sandhi interacts with speed and/or how nuances of speaker attitude are expressed in them (what we do with rythm/inflection/sentence-intonation and stress in Eng., and with particles and ??? in e.g. Cantonese) please chime in or call me (415-608-0564) so I can convey your wisdom. [also looking for a from-scratch Arabic partner]<br />
:'''(TBD)''': [[Getting started with Arduino]]<br />
:'''(TBD)''': [[Distributed Databases]]<br />
:'''(TBD)''': [[Scrum Club]] - I though I'd test the waters and see if anyone was interested in a noisebridge scrum club details are here http://scrumclub.org/scrum-clubs/ if inturested hit me up twitter: @theabcasian, facebook: http://www.facebook.com/theabcasian<br />
:'''(TBD)''': [[CNC Mill Workshop]] - Who wants to make stuff on the [[MaxNCMill]]?<br />
:'''(TBD)''': [[Math &amp; Science Help]] - If you would like some math, science or engineering help, I'm down to lend a hand.<br />
:'''(TBD)''': [[Cyborg Group|Cyborg Group / Sensebridge]] - Work on projects like artificial senses. Someone needs to lead this!<br />
:'''(TBD)''': [[OpenEEG]] - Brain tech. Has historically met on Sundays, at the behest of interested parties.<br />
:'''(TBD)''': [[Programming_for_Poets | Programming for Poets]] - Gentle intro to programming using Processing<br />
<br />
= Past Events =<br />
===2010===<br />
* '''Sunday, August 22, 19:00 CLUB-MATE DROPOFF AND TASTING PARTY''' Nick Farr will be in town to drop off Club-Mate ordered by San Franciscans!<br />
* '''June 5th, 12:00-19:00 - [[NoiseBridgeRehab]]''' - Help make the space more usable and accessible! Noisebridge needs your help!<br />
* '''June 5th, 16:00-20:00 - [[Science For Juggalos]]''' - Science Fair in front of the Warfield Theater teaching magnetism to Juggalos<br />
* '''June 6th, 15:00 - [[AVC Meetup]]''' - Entrepreneurial bonding &amp; matchmaking<br />
* '''June 9th, 21:00 - Your liver supports Noisebridge''' - Come to Elixir @ 16th &amp; Guerrero anytime after 21:00 and drink, drink, drink! 50% of tips go to Noisebridge<br />
* '''February 27th, 20:00 - [[Hacker EPROM]]''' - Noisebridge's first prom! Nice tie and a (robot) date required. We will have a DJ and punch.<br />
* '''February 24th, 19:00, Wednesday - Joris Peels, of [http://www.shapeways.com Shapeways]''', and expert on 3D printing, will give a [[ShaperwaysPresentation | talk and demonstration]] at Noisebridge!.<br />
* '''February 23rd, 18:00 - Cleaning day''' - Come and help clean Noisebridge, because everyone loves a clean hack space.<br />
* '''February 12th, 21:00 - visit from Steve Jackson'''. Game designer [http://en.wikipedia.org/wiki/Steve_Jackson_%28US_game_designer%29 Steve Jackson], founder of Steve Jackson Games, will visit Noisebridge.<br />
* '''January 27th, 18:00-20:00 - [[beatrixjar event|Circuit Bending Workshop]]''' - [http://www.beatrixjar.com/ Beatrix*JAR] (contact [[User:Gpvillamil|Gian Pablo]] for more info)<br />
* '''January 27th, 20:00-22:00 - [[beatrixjar event|Circuit Bending Performance]]''' - [http://www.beatrixjar.com/ Beatrix*JAR] - &quot;Celebrate a night of new sound that will change your idea of music forever!&quot;<br />
* '''January 25th, 19:30 - [[Bag Porn]]''' - What's in your bag?<br />
* '''January 20th, 19:00-21:00 - [http://groups.google.com/group/bacat/about Bay Categories &amp; Types]''' - Categories, monoids, monads, functors and more! Held in the Alonzo Church classroom.<br />
* '''January 20th, 19:00 - [[User Experience Book Club SF]]''' - Our book this month is &quot;A Theory of Fun for Game Design&quot; by Raph Koster - http://is.gd/6sEqw (meets in Turing)<br />
* '''January 21st, 20:00 - [[Five Minutes of Fame]]''' - Monthly set of lightning talks on diverse topics<br />
* '''January 22nd, 17:00 - [[CleaningParty| Cleaning Party]]''' - Come help clean up Noisebridge! Awsum fun!<br />
* ...January 14th,16th, and 17th 1:00- ??? Build Out day for kitchen/bathroom/laundry bring yourself and a good attitude, learn a few things as well<br />
* '''January 15th, 18:00 - [[CNC_Mill_Workshop]]''' - Learn to use the CNC mill for 2D engraving and circuit board routing<br />
* Thursdays 17:00 [[ASL Group|American Sign Language]] - Learn how to talk without using your voice (or just come chat in ASL). &lt;small&gt;[http://whenisgood.net/noisebridge/asl/generic click to reschedule]&lt;/small&gt;<br />
<br />
===2009===<br />
* '''November 18th, 19:30''' - [[Dorkbot_2009_11_18|Dorkbot]]<br />
* '''November 19th, 18:00''' - [[Mesh meetup]]<br />
* '''November 19th, 20:00''' - [[Five Minutes of Fame]]<br />
* '''November 20th, 18:00''' - Loud Objects [http://www.flickr.com/photos/createdigitalmedia/3428249036/ Noise Toy workshop].<br />
* '''November 20th, 20:00''' - Performance by [http://www.loudobjects.com/ Loud Objects], (featuring Tristan Perich and Lesley Flanigan) and [http://www.myspace.com/jibkidder Jib Kidder].<br />
:'''2009-11-05''' - [http://www.server-sky.com/ Server Sky presentation: Internet and Computation in Orbit] by Keith Lofstrom<br />
:'''2009-11-05''' - [[Mesh meetup]]<br />
:'''2009-11-02''' - [[French]] book club meeting to discuss [http://www.amazon.com/exec/obidos/tg/detail/-/2842612892/ref=ord_cart_shr?_encoding=UTF8&amp;m=ATVPDKIKX0DER&amp;v=glance Une Si Longue Lettre]<br />
: ''' October 1st, 18:00''' - [[Wireless_Mesh_Network_Meetup | Mesh wireless meetup]]<br />
: ''' October 1st, 19:00''' - [http://groups.google.com/group/bacat Bay Area Categories and Types]<br />
: '''2009-10-03''' [[Year 1 Open Hacker House]]<br />
:'''Friday''': [[CrazyCryptoNight]] - Discussion of cryptography for beginners through experts. 6-???<br />
:'''Sunday''' : [[OpenEEG | OpenEEG Hacking]] Sundays, at 3-5pm.<br />
:'''Tuesday''': [[Haskell/Haschool]] - Learn Haskell with Jason Dusek. 6PM - 7:30PM, from May until we're all experts.<br />
:'''Wednesday''': [[Adobe_Lightroom|Adobe Lightroom]] - Become a more organized photographer. Weekly class (mostly held off site).<br />
:'''Thursday''': [[Professional VFX Compositing With Adobe After Effects]] - Taught by [[User:SFSlim|Aaron Muszalski]]. 7:30PM - 10PM, most Thursdays in May &amp; June &amp; ? (click through dammit)<br />
:'''2009-09-17''': [[Five Minutes of Fame]] 3D Edition<br />
:'''2009-09-17''': [[Wireless Mesh Network Meetup | Mesh wireless meetup]]<br />
:'''2009-08-20''': [[Five Minutes of Fame]] One Dee Edition<br />
:'''2009-07-16''': [[Five Minutes of Fame]] Zero Dee<br />
:'''2009-07-02 - 2009-07-05''': [http://toorcamp.org Toorcamp]<br />
:'''2009-07-01''': Noisedroid meeting to discuss location logging on Android platform (and other stuff too, I'm sure)<br />
:'''2009-06-30''': [[Powerbocking Class|Powerbocking class]]<br />
:'''2009-06-30''': &quot;Suing Telemarketers for Fun and Profit&quot; (Toorcamp talk preview)<br />
:'''2009-06-28''': &quot;Meditation for Hackers&quot; (Toorcamp workshop preview)<br />
:'''2009-06-18''': [[Five Minutes of Fame]]<br />
:'''2009-06-15''': [[Eagle Workshop]] Session two of the Eagle CAD workshop.<br />
:'''2009-06-13''': [[RoboGames 2009]] Noisebridge had a booth staffed by vounteers, great fun!<br />
:'''2009-05-21''': [[Five Minutes of Fame]]<br />
:'''2009-04-27''': [[EagleCAD workshop]] -- learn to use this CAD tool for printed circuit board design<br />
:'''2009-04-16''': [[Five Minutes of Fame]] April showers &amp; flowers edition<br />
:'''2009-04-11''': [[RFID Hacking]] weekend workshop (this event moved from the original March date)<br />
:'''2009-04-05''': [[First aid and CPR class]] Learning how to not only not die, but also reduce scarring!<br />
:'''2009-04-03''': [[Sudo pop]] 2PM and on. Making the first batch of a Noisebridge label yerba mate-niated rootbrew, gratis and DIY<br />
:'''2009-03-26''': [[OpenEEG | OpenEEG Hacking]] first meet up for this new group: 8 pm<br />
:'''2009-03-19''': [[Five Minutes of Fame]]<br />
:'''2009-03-12''': [[OpenBTS and GSM]] talk by David Burgess<br />
:'''2009-02-14''': [[Open Heart Workshop]] Valentine's Day blinkyheart soldering party! <br />
:'''2009-02-13''': [[Time-t_Party|&lt;tt&gt;time_t&lt;/tt&gt; Party]] to celebrate 1,234,567,890 since the Unix epoch.<br />
:'''2009-02-09''': [[Spanish learning at 8:30]]<br />
:'''2009-02-05''': [[PGP Key Workshop]]<br />
:'''2009-01-31''': [[Locksport and Lockpicking]]<br />
<br />
===2008===<br />
:'''2008-12-27''': [[25C3]] Chaos Computer Congress in Berlin<br />
:'''2008-12-20 &amp; 21''': [[Creme Brulee]] Workshop on creating a french dessert, with bonus propane torch.<br />
:'''2008-12-17 20:00''': [[Machine Learning]] Birds-of-a-feather<br />
:'''2008-11-24''': [[Circuit Hacking Monday]] circuit design workshop<br />
:'''2008-11-21, 7pm''':[[Milk and Cookies]] -- [[User:Dmolnar|David Molnar]] hosts Milk and Cookies at 83C. Bring a short 5-7minute thing to read to others. Bring a potluck cookie/snack/drink if you like. David will bring milk and cookies.<br />
:'''2008-11-17, 7:30pm''': [[Basic Bicycle Maintain]] - [[User:rubin110|Rubin]] and [[User:rigel|rigel]] hate it when we see a bike that isn't maintained. Screechy chains and clacking derailleur can go to hell. Basic bike tune up, sharing the smarts on simple things you can do at home to make your ride suck a whole lot less.<br />
:'''2008-11-16, 5:00pm''': [[RepRap Soldering Party]] - help assemble RepRap! RSVPs required on wiki! [[User:Adi|adi]]<br />
:'''2008-11-16, 3:00pm''': [[Oscilloscopes]] - Learn how to use this versatile tool to test electronic circuits. Maximum 6 slots, please sign up ahead of time! [[User:dstaff|dstaff]]<br />
:'''2008-10-31''': [[Halloween Open House]] - NoiseBridge's own [[PPPC]] threw an awesome open house/halloween gala. Post pictures if you got 'em!<br />
:'''2008-10-25''': [[Soldering Workshop]] and Pumpkin Hackin' - Learn to solder for total newbies (or learn to solder better!), including surface mount. Additionally, carve your halloween pumpkins and enjoy some experimental pumpkin pie and/or soup.<br />
:'''2008-10-07''': (tuesday before meeting) - Etch a circuit board. I'll be trying a photo resist etching and a basic printed mask etching. This is step 1/3 for a project called &quot;annoying USB thingie&quot; which will execute pre-defined keystrokes by sneaking a tiny USB dongle onto a victim^h^h^h^h^h buddy's computer.<br />
:'''2008-09-13''': [[Processing Workshop]] — Learn this very easy-to-use programming language! - [[Processing Workshop Report]]<br />
:'''2008-02-16''': [[Brain Machine Workshop|Brain Machine Making Workshop]]: Our first hardware sprint!</div>Turbclnthttps://noisebridge.net/wiki/Fermentation_logsFermentation logs2011-03-09T08:54:12Z<p>Turbclnt: </p>
<hr />
<div>= March 9th, 2011: (yet unnamed) v0.1 =<br />
<br />
== Ingredients and Batch Size ==<br />
* Yeast type &amp; origin: '''[[Fermenting Yeasts#Gert Strand, Black Label|Gert Strand, Black Label]]''' (Malmo, Sweden)<br />
* Theoretical %ABV: 14-17%<br />
* Sugar Source: TBD<br />
* Target Size: ~25L<br />
<br />
<br />
<br />
= March 2nd, 2011: DAVROS v0.1 =<br />
<br />
== Ingredients and Batch Size ==<br />
* Yeast type &amp; origin: '''[[Fermenting Yeasts#Gert Strand, Black Label|Gert Strand, Black Label]]''' (Malmo, Sweden)<br />
* Theoretical %ABV: 14-17%<br />
* Sugar Source: C&amp;H Cane Sugar<br />
* Target Size: ~25L<br />
<br />
== Fermenting Log ==<br />
*'''03/02/2011 20:05''': C&amp;H Cane Sugar has been dissolved and diluted to 2x 12.5L. Temps: 24.5C, 25.5C. Confirmed ready to pitch yeast.<br />
*'''03/02/2011 20:50''': Yeast was pitched and shaken to dissolve into a cloudy solution. Specific gravity of each tank = 1.090 (exactly equal to yeast maker's recommendation).<br />
*'''03/03/2011 23:59''': Davros tank 1&amp;2: 72 degrees [[User:Miloh|Miloh]]<br />
*'''03/04/2011 13:13''': Davros tank 1&amp;2: 72 degrees<br />
*'''03/08/2011 20:35''': Davros tank 1: 67C, specific gravity = 984.5 (target range = 984 - 987). Its done! [[User:turbclnt|Sean C]]<br />
*'''03/08/2011 20:35''': Davros tank 2: 67C. specific gravity = 984.0 (target range = 984 - 987). Its done too! [[User:turbclnt|Sean C]]</div>Turbclnthttps://noisebridge.net/wiki/Fermenting_YeastsFermenting Yeasts2011-03-02T01:50:55Z<p>Turbclnt: Created page with '=Fermenting Yeasts= ==Gert Strand, Black Label== ===General Info=== This is a yeast I've been wanting to try for awhile. It starts sterile, so no need for special sterilization …'</p>
<hr />
<div>=Fermenting Yeasts=<br />
<br />
==Gert Strand, Black Label==<br />
===General Info===<br />
This is a yeast I've been wanting to try for awhile. It starts sterile, so no need for special sterilization needs to happen in the ferment tank. Also, it should decrease the amount of volatiles coming from the incorrect micro organisms. The yeast is a completely natural strain - very little has been done other than selective breeding to ensure the correct yeast comes out in the end. This particular strain has all the nutrients included to ensure anaerobic fermentation. This particular strain handles scaling well because it generates less heat on fermenting, and also less off gassing. Lastly, this strain can tolerate a pretty high alcohol content when compared to standard baker's yeast.<br />
<br />
===The Numbers===<br />
* Theoretical ABV: 14-17 vol%<br />
* Optimal temperature: 20-30°C<br />
* Killing temperature chart:<br />
{| class=&quot;wikitable&quot;<br />
|-<br />
! % ABV<br />
! Kill Temp<br />
|-<br />
| 11%<br />
| 35°C<br />
|-<br />
| 12%<br />
| 34,5°C<br />
|-<br />
| 13%<br />
| 34°C<br />
|-<br />
| 14%<br />
| 33,5°C<br />
|-<br />
| 15%<br />
| 33°C<br />
|-<br />
| 16%<br />
| 29°C<br />
|-<br />
| 16,5%<br />
| 22°C<br />
|}<br />
<br />
* Starting Specific Gravity = 1090<br />
* Ending Specific Gravity = 984 - 987<br />
<br />
===Instructions===<br />
* Dissolve 6kg sugar into 8L hot water. Stir until completely dissolved<br />
* Top up to 25L with cold water<br />
* Allow pot to cool to 39C or below before continuing<br />
* Add 1 sachet (90g) turbo yeast and stir until no more yeast particles are visible. Specific Gravity should be 1090.<br />
* Allow to ferment open at 20-30C. Targeted completion time is 2-5 days<br />
* End Condition: Specific Gravity = 984 - 987</div>Turbclnt